Variant report

Variant	rs7531027
Chromosome Location	chr1:62496902-62496903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62495138..62497072-chr1:62504088..62506298,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236646	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10493313	0.81[EUR][1000 genomes]
rs11576777	1.00[JPT][hapmap]
rs11577828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11579010	1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs11581307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11585888	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11587128	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11590485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11590812	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11590954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1332631	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1363	0.93[ASN][1000 genomes]
rs1412620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122938	1.00[CHB][hapmap]
rs17123017	1.00[CHB][hapmap]
rs17313395	1.00[JPT][hapmap]
rs17378995	1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2067881	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2067882	1.00[CHB][hapmap]
rs2365985	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2476180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3762449	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs41394744	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4325166	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4915603	0.93[ASN][1000 genomes]
rs4915795	0.93[ASN][1000 genomes]
rs56379320	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61777665	0.93[ASN][1000 genomes]
rs61777666	0.93[ASN][1000 genomes]
rs6661849	1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs6673889	1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs6682776	1.00[MEX][hapmap]
rs6685356	0.86[EUR][1000 genomes]
rs6685442	1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6697273	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7519802	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7528431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7539653	1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7531027	NFIA	cis	cerebellum	SCAN
rs7531027	TACSTD2	cis	cerebellum	SCAN
rs7531027	RAVER2	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
2	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:62459000-62516000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:62459200-62511200	Weak transcription	Gastric	stomach
6	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:62460000-62499600	Weak transcription	Fetal Intestine Large	intestine
8	chr1:62460000-62516400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:62460200-62516000	Weak transcription	HMEC	breast
11	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:62474200-62518600	Weak transcription	Primary T cells from cord blood	blood
13	chr1:62480600-62513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:62484400-62523000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:62484600-62506000	Weak transcription	NHEK	skin
17	chr1:62484800-62511200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:62486200-62517600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:62488000-62498000	Weak transcription	Fetal Heart	heart
20	chr1:62488400-62497600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:62488400-62497600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:62488400-62521200	Weak transcription	Ovary	ovary
23	chr1:62488600-62499000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:62490600-62499200	Weak transcription	Right Atrium	heart
25	chr1:62491800-62499200	Weak transcription	Left Ventricle	heart
26	chr1:62491800-62511200	Weak transcription	Psoas Muscle	Psoas
27	chr1:62494600-62504600	Weak transcription	Aorta	Aorta
28	chr1:62494600-62511200	Weak transcription	Fetal Intestine Small	intestine
29	chr1:62494600-62524400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:62494600-62524400	Weak transcription	Esophagus	oesophagus
31	chr1:62494800-62497800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:62494800-62498400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:62494800-62498600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:62494800-62505200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:62495000-62497800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:62495000-62499000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:62495000-62504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:62495000-62515200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:62495200-62516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:62495200-62544800	Weak transcription	Liver	Liver
41	chr1:62495600-62497400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:62495800-62497400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:62496200-62504600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:62496600-62497200	Enhancers	Primary B cells from cord blood	blood
45	chr1:62496600-62500400	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr1:62496800-62497400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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