Variant report

Variant	rs165257
Chromosome Location	chr1:180204618-180204619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180176758..180178917-chr1:180204448..180206971,2	K562	blood:
2	chr1:180197834..180202182-chr1:180202469..180206213,5	K562	blood:
3	chr1:180202900..180206248-chr1:180207792..180211667,4	K562	blood:
4	chr1:180202741..180204751-chr1:180205001..180207595,2	K562	blood:

Variant related genes	Relation type
ENSG00000121454	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11583176	0.80[EUR][1000 genomes]
rs12407014	0.87[ASN][1000 genomes]
rs164982	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs355614	0.81[AMR][1000 genomes]
rs355615	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs355627	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs355632	0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs355633	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs355636	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs357069	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs357074	0.91[ASN][1000 genomes]
rs357077	0.93[ASN][1000 genomes]
rs3842831	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3856050	0.84[EUR][1000 genomes]
rs4652492	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6425616	0.82[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6425617	0.89[ASN][1000 genomes]
rs7529839	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539240	0.87[ASN][1000 genomes]
rs7539244	0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]

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	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
12	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
13	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
14	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
15	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
16	nsv466239	chr1:180145978-180268476	Bivalent Enhancer ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised 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
17	nsv548345	chr1:180145978-180268476	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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
18	nsv1005793	chr1:180150400-180205202	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
19	nsv1005073	chr1:180152550-180250783	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
20	nsv535219	chr1:180152550-180250783	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
21	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	nsv498075	chr1:180179441-180278544	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv872575	chr1:180186713-180238243	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs165257	XPR1	cis	cerebellum	SCAN
rs165257	RFWD2	cis	cerebellum	SCAN
rs165257	QSOX1	cis	parietal	SCAN
rs165257	RABGAP1L	cis	parietal	SCAN
rs165257	RASAL2	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180200800-180205600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr1:180201000-180205400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
3	chr1:180201000-180205600	Bivalent Enhancer	Fetal Stomach	stomach
4	chr1:180201200-180204800	Bivalent Enhancer	Brain Germinal Matrix	brain
5	chr1:180202200-180205200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
6	chr1:180202200-180205600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:180202200-180205600	Enhancers	Pancreas	Pancrea
8	chr1:180202200-180205800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr1:180202200-180206200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr1:180202400-180205400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr1:180202400-180205400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr1:180202400-180205400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:180202400-180205400	Bivalent Enhancer	Left Ventricle	heart
14	chr1:180202600-180205600	Bivalent Enhancer	Spleen	Spleen
15	chr1:180202600-180205800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr1:180202800-180205000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:180202800-180205400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:180202800-180205800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:180203000-180204800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
20	chr1:180203200-180205000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr1:180203200-180205400	Bivalent Enhancer	Stomach Mucosa	stomach
22	chr1:180203400-180204800	Bivalent Enhancer	Lung	lung
23	chr1:180203400-180204800	Bivalent Enhancer	NHDF-Ad	bronchial
24	chr1:180203400-180205000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:180203400-180205000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:180203400-180205000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:180203400-180205000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
28	chr1:180203400-180205000	Bivalent Enhancer	Esophagus	oesophagus
29	chr1:180203400-180205400	Bivalent Enhancer	Fetal Brain Female	brain
30	chr1:180203400-180205400	Bivalent Enhancer	Fetal Heart	heart
31	chr1:180203400-180205400	Enhancers	Gastric	stomach
32	chr1:180203600-180205000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:180203600-180205000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:180203600-180205000	Bivalent Enhancer	HUVEC	blood vessel
35	chr1:180203600-180205200	Bivalent Enhancer	Fetal Brain Male	brain
36	chr1:180203600-180205400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:180203600-180205400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:180203600-180206600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr1:180203800-180205000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr1:180203800-180205400	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr1:180204000-180204800	Bivalent Enhancer	Placenta	Placenta
42	chr1:180204000-180205000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr1:180204000-180205000	Bivalent Enhancer	Primary B cells from cord blood	blood
44	chr1:180204000-180205200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr1:180204000-180205400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr1:180204000-180205400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:180204000-180205600	Bivalent Enhancer	Liver	Liver
48	chr1:180204200-180205000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
49	chr1:180204200-180205000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:180204200-180205000	Bivalent Enhancer	Right Atrium	heart

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