Variant report

Variant	rs9865971
Chromosome Location	chr3:141237859-141237860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141205718..141209155-chr3:141236007..141238625,3	MCF-7	breast:
2	chr3:141237293..141240877-chr3:141241422..141245605,3	K562	blood:
3	chr3:141203748..141207379-chr3:141236943..141239708,3	K562	blood:

Variant related genes	Relation type
ENSG00000250170	Chromatin interaction
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1077181	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs11557453	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707656	0.85[EUR][1000 genomes]
rs11708253	0.83[EUR][1000 genomes]
rs11709875	0.96[CEU][hapmap];0.93[MEX][hapmap]
rs11711318	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713714	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11714208	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11716776	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11717144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717842	0.96[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12695734	0.83[EUR][1000 genomes]
rs12695735	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs12695736	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12695740	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12695741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12695743	0.86[ASW][hapmap];0.92[CEU][hapmap];0.81[GIH][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13059128	0.83[CEU][hapmap];0.93[MEX][hapmap]
rs13062809	0.87[ASN][1000 genomes]
rs13067519	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13068454	0.80[EUR][1000 genomes]
rs13072100	0.96[CEU][hapmap];0.85[MEX][hapmap];0.85[EUR][1000 genomes]
rs13078872	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13083593	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13084444	0.96[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13088429	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs13095168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863870	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs2312194	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34317570	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34342794	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732872	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3806647	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4334619	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6769161	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs71619392	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs720663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624941	1.00[JPT][hapmap]
rs7636914	0.85[MEX][hapmap]
rs7649666	1.00[JPT][hapmap]
rs7651511	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9289629	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9289634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9808953	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];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9822575	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9823528	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9829588	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9830055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9833121	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9836050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836818	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837202	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs9838230	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838419	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9840159	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9840697	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9849180	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9850416	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9851256	1.00[CHB][hapmap]
rs9868956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9870749	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9873042	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006237	chr3:141227525-141300722	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1014365	chr3:141235379-141282615	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9865971	GK5	cis	parietal	SCAN
rs9865971	RASA2	cis	cerebellum	SCAN
rs9865971	ZBTB38	cis	cerebellum	SCAN
rs9865971	ATP1B3	cis	cerebellum	SCAN
rs9865971	RASA2	cis	parietal	SCAN
rs9865971	ACPL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141207000-141255000	Weak transcription	Aorta	Aorta
2	chr3:141210400-141248000	Weak transcription	NHLF	lung
3	chr3:141216000-141239600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:141217800-141258400	Weak transcription	Psoas Muscle	Psoas
5	chr3:141226600-141254400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:141227400-141242800	Weak transcription	Ovary	ovary
7	chr3:141228400-141246600	Strong transcription	Dnd41	blood
8	chr3:141229400-141267400	Weak transcription	Fetal Heart	heart
9	chr3:141230000-141259800	Weak transcription	Small Intestine	intestine
10	chr3:141230400-141243000	Weak transcription	Spleen	Spleen
11	chr3:141231000-141243000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:141231200-141240200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:141231200-141240800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:141231200-141245000	Strong transcription	Fetal Thymus	thymus
15	chr3:141231600-141254400	Weak transcription	Fetal Kidney	kidney
16	chr3:141231600-141263600	Weak transcription	Fetal Brain Male	brain
17	chr3:141231800-141242600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:141232000-141241800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:141232200-141245600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:141232200-141254400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:141232400-141240000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:141232600-141239600	Strong transcription	Osteobl	bone
23	chr3:141232600-141244400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:141232800-141239600	Strong transcription	Primary T cells from cord blood	blood
25	chr3:141232800-141240000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:141234000-141254400	Weak transcription	Right Ventricle	heart
27	chr3:141235200-141238400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:141235400-141239800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:141235600-141238200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr3:141235800-141239200	Weak transcription	NHEK	skin
31	chr3:141235800-141240000	Strong transcription	NHDF-Ad	bronchial
32	chr3:141236200-141238000	Strong transcription	HMEC	breast
33	chr3:141236200-141242800	Weak transcription	Hela-S3	cervix
34	chr3:141236200-141281600	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:141236400-141238000	Weak transcription	HSMM	muscle
36	chr3:141236400-141238400	Weak transcription	Fetal Lung	lung
37	chr3:141236400-141238800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:141236400-141239200	Weak transcription	NH-A	brain
39	chr3:141236400-141240400	Strong transcription	Primary B cells from cord blood	blood
40	chr3:141236400-141241000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:141236400-141241200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:141236400-141242800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:141236400-141243400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:141236400-141244200	Weak transcription	Pancreas	Pancrea
45	chr3:141236400-141245200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:141236400-141249000	Weak transcription	Right Atrium	heart
47	chr3:141236400-141254400	Weak transcription	Brain Angular Gyrus	brain
48	chr3:141236400-141254400	Weak transcription	Left Ventricle	heart
49	chr3:141236400-141276000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:141236400-141301000	Weak transcription	Brain Substantia Nigra	brain

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