Variant report

Variant	rs3842888
Chromosome Location	chr1:180129205-180129206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180049619..180051406-chr1:180127206..180129777,2	MCF-7	breast:
2	chr1:180121054..180127420-chr1:180128164..180132367,10	K562	blood:
3	chr1:180127970..180130993-chr1:180131088..180133092,3	K562	blood:

Variant related genes	Relation type
ENSG00000116260	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10913936	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12075337	0.81[CHB][hapmap]
rs2298206	0.81[CHB][hapmap]
rs2319653	0.86[ASW][hapmap];0.80[LWK][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs3753797	0.81[CHB][hapmap]
rs3753802	0.84[ASN][1000 genomes]
rs3753803	0.89[CHD][hapmap]
rs3767183	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs3767184	0.86[CEU][hapmap]
rs3767191	0.91[ASN][1000 genomes]
rs3820305	0.86[CEU][hapmap]
rs3820308	0.87[CHB][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56158647	0.86[EUR][1000 genomes]
rs6689602	0.81[CHB][hapmap]
rs6703180	0.89[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3842888	QSOX1	cis	Whole Blood	GTEx
rs3842888	ZNF648	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180124600-180129400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:180124800-180151000	Weak transcription	Aorta	Aorta
3	chr1:180125000-180129400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:180125000-180133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:180125000-180136000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:180125200-180129600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:180125200-180134600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:180125200-180137400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:180125200-180150400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:180125400-180130800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:180125400-180134800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:180125600-180129400	Weak transcription	Fetal Thymus	thymus
13	chr1:180125600-180133200	Weak transcription	Thymus	Thymus
14	chr1:180125600-180136400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:180125600-180159200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:180125800-180129600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:180125800-180135800	Weak transcription	Primary T cells from cord blood	blood
18	chr1:180126000-180132600	Weak transcription	Primary B cells from cord blood	blood
19	chr1:180126000-180135600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:180126000-180136800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:180126000-180151000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:180126000-180151400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:180126200-180131600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:180126200-180133600	Weak transcription	Brain Germinal Matrix	brain
25	chr1:180126200-180136600	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:180126200-180152400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:180126400-180153800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:180126600-180129600	Weak transcription	Brain Substantia Nigra	brain
29	chr1:180126600-180129800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:180126600-180131600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:180126600-180134400	Weak transcription	Brain Angular Gyrus	brain
32	chr1:180126600-180135600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:180126600-180135600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:180126800-180129600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:180126800-180131600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:180126800-180131800	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr1:180126800-180132400	Enhancers	Stomach Mucosa	stomach
38	chr1:180126800-180134800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:180126800-180135000	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr1:180126800-180135800	Weak transcription	Hela-S3	cervix
41	chr1:180127200-180130000	Strong transcription	NHEK	skin
42	chr1:180127200-180133400	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:180127200-180134000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:180127200-180134600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:180127200-180136000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:180127200-180137400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:180127200-180140400	Weak transcription	GM12878-XiMat	blood
48	chr1:180127400-180142800	Weak transcription	HSMM	muscle
49	chr1:180127600-180130600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:180127600-180134400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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