Variant report

Variant	rs6690609
Chromosome Location	chr1:180136504-180136505
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180136376..180137428-chr1:180197371..180198301,4	MCF-7	breast:
2	chr1:179848457..179853504-chr1:180134970..180139712,7	MCF-7	breast:
3	chr1:179864493..179866934-chr1:180134864..180137550,2	MCF-7	breast:
4	chr1:180048120..180049622-chr1:180134453..180137364,2	MCF-7	breast:
5	chr1:180136376..180137616-chr1:180197323..180198301,4	MCF-7	breast:
6	chr1:180123373..180126275-chr1:180136123..180139558,3	K562	blood:
7	chr1:180103401..180107232-chr1:180135881..180138747,3	MCF-7	breast:
8	chr1:180135428..180138250-chr1:180150894..180153157,2	MCF-7	breast:
9	chr1:180091209..180093706-chr1:180135301..180137840,3	MCF-7	breast:
10	chr1:180136278..180138726-chr1:180139135..180141968,2	K562	blood:
11	chr1:180111136..180114017-chr1:180135288..180137441,2	K562	blood:
12	chr1:180132376..180134766-chr1:180135945..180137966,2	K562	blood:
13	chr1:180045161..180048156-chr1:180135974..180138865,2	MCF-7	breast:
14	chr1:180133624..180140712-chr1:180197495..180201623,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000116260	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000261817	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000121454	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10913944	1.00[CEU][hapmap]
rs12741050	1.00[CEU][hapmap]
rs17371594	1.00[CHD][hapmap]
rs3843273	1.00[CEU][hapmap]
rs6425611	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1007590	chr1:180121480-180236452	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv999104	chr1:180121480-180242659	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1011933	chr1:180125666-180171361	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv1007334	chr1:180126438-180191251	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv1006153	chr1:180127036-180171361	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv1013314	chr1:180127036-180187922	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv1002133	chr1:180127036-180230081	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv1008644	chr1:180127616-180171361	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
17	nsv1009112	chr1:180127616-180176979	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
18	nsv1004421	chr1:180127616-180187922	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
19	nsv1000954	chr1:180127616-180191251	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
20	nsv999247	chr1:180127616-180196068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
21	nsv1011134	chr1:180127616-180201104	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
22	nsv999182	chr1:180127616-180236452	Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
23	nsv1005512	chr1:180127616-180242659	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
24	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
25	nsv1014345	chr1:180132688-180171361	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
26	nsv1009958	chr1:180132688-180176979	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
27	nsv1001540	chr1:180132688-180180056	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
28	nsv1001909	chr1:180132688-180187922	Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
29	nsv1011191	chr1:180132688-180191251	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
30	nsv1002768	chr1:180132688-180195394	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
31	nsv1007515	chr1:180132688-180196068	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
32	nsv1012816	chr1:180132688-180201104	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
33	nsv1012145	chr1:180132688-180236452	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
34	nsv1000781	chr1:180133856-180171361	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
35	nsv1005030	chr1:180133856-180191251	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6690609	QSOX1	cis	Whole Blood	GTEx
rs6690609	XPR1	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180124800-180151000	Weak transcription	Aorta	Aorta
2	chr1:180125200-180137400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:180125200-180150400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:180125600-180159200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:180126000-180136800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:180126000-180151000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:180126000-180151400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:180126200-180136600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:180126200-180152400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:180126400-180153800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:180127200-180137400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:180127200-180140400	Weak transcription	GM12878-XiMat	blood
13	chr1:180127400-180142800	Weak transcription	HSMM	muscle
14	chr1:180127600-180137400	Weak transcription	K562	blood
15	chr1:180127600-180142600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:180127800-180136600	Weak transcription	HUVEC	blood vessel
17	chr1:180127800-180136800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:180127800-180137200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:180128600-180137000	Weak transcription	Fetal Intestine Large	intestine
20	chr1:180130000-180137000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:180132800-180140600	Enhancers	Stomach Mucosa	stomach
22	chr1:180133000-180137200	Enhancers	Right Ventricle	heart
23	chr1:180133000-180138000	Enhancers	Pancreas	Pancrea
24	chr1:180133000-180138200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:180133000-180139400	Enhancers	Left Ventricle	heart
26	chr1:180133000-180143800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:180133200-180139400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:180133400-180136600	Enhancers	Psoas Muscle	Psoas
29	chr1:180133400-180153200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:180133600-180136800	Strong transcription	Fetal Intestine Small	intestine
31	chr1:180133800-180136600	Weak transcription	Spleen	Spleen
32	chr1:180133800-180152800	Weak transcription	Primary B cells from cord blood	blood
33	chr1:180134000-180136600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:180134000-180167600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:180134200-180137400	Enhancers	HSMMtube	muscle
36	chr1:180134200-180138800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:180134400-180136600	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:180134400-180136800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr1:180134400-180136800	Enhancers	Brain Substantia Nigra	brain
40	chr1:180134400-180137000	Genic enhancers	Fetal Brain Female	brain
41	chr1:180134400-180137000	Enhancers	Ovary	ovary
42	chr1:180134400-180139000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:180134400-180139600	Genic enhancers	Gastric	stomach
44	chr1:180134400-180140600	Genic enhancers	Lung	lung
45	chr1:180134400-180141000	Enhancers	Right Atrium	heart
46	chr1:180134400-180168800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:180134600-180136800	Enhancers	Brain Cingulate Gyrus	brain
48	chr1:180134600-180137200	Genic enhancers	Fetal Stomach	stomach
49	chr1:180134600-180138400	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr1:180134600-180138800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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