Variant report

Variant	rs17125137
Chromosome Location	chr12:51365006-51365007
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51363073..51365710-chr12:51419692..51421851,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1005559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1048230	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506298	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506299	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169626	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169633	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169636	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169637	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169639	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169641	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169644	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169646	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11169647	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169648	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169649	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169654	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169655	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169661	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169667	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169669	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169670	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169671	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169672	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169682	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11519977	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831810	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11831946	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs11833022	0.87[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs12366476	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12366756	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12369278	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12369639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12369658	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12369666	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12370820	0.83[EUR][1000 genomes]
rs12371463	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12372173	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12809563	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12810174	0.81[EUR][1000 genomes]
rs12810596	0.81[EUR][1000 genomes]
rs12810659	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811508	0.81[CEU][hapmap]
rs12811658	0.81[EUR][1000 genomes]
rs12811684	0.81[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs12811777	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12812650	0.82[EUR][1000 genomes]
rs12812727	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12813309	0.81[EUR][1000 genomes]
rs12813368	0.81[EUR][1000 genomes]
rs12813728	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12817386	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818033	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12819296	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12820966	0.81[EUR][1000 genomes]
rs12821444	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12822509	0.82[EUR][1000 genomes]
rs12824225	0.82[EUR][1000 genomes]
rs12824840	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12824958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12826153	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs12827861	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12828349	0.82[EUR][1000 genomes]
rs12828536	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12830048	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830073	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12830422	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12831269	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12831597	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs15897	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17296192	0.81[CEU][hapmap]
rs224565	0.90[ASN][1000 genomes]
rs224577	0.81[ASN][1000 genomes]
rs224589	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs224591	0.87[ASN][1000 genomes]
rs2285228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285230	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301529	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516742	0.86[ASN][1000 genomes]
rs2630364	0.89[ASN][1000 genomes]
rs319932	0.90[ASN][1000 genomes]
rs34514224	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34735738	0.82[EUR][1000 genomes]
rs35037088	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35262273	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35379220	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35656976	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35999440	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs407135	0.87[ASN][1000 genomes]
rs422637	0.86[ASN][1000 genomes]
rs422982	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs440595	0.84[ASN][1000 genomes]
rs4444142	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4471501	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs454520	0.87[ASN][1000 genomes]
rs4768964	0.80[EUR][1000 genomes]
rs4768967	0.80[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs6580784	0.81[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs6580792	0.81[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap]
rs6580793	0.81[CEU][hapmap]
rs67025973	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67133203	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67259551	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67260912	0.81[EUR][1000 genomes]
rs706801	0.93[ASN][1000 genomes]
rs706802	0.93[ASN][1000 genomes]
rs7135059	0.83[EUR][1000 genomes]
rs71445768	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71445772	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7305638	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7306293	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73090655	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7954140	0.81[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs7959075	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7959082	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7964570	0.81[EUR][1000 genomes]
rs7965566	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972406	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7975147	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7976777	0.81[EUR][1000 genomes]
rs7977104	0.85[GIH][hapmap]
rs7978723	0.87[CEU][hapmap];0.88[GIH][hapmap];0.80[EUR][1000 genomes]
rs7980874	0.83[EUR][1000 genomes]
rs829022	0.93[ASN][1000 genomes]
rs853235	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs970098	0.81[EUR][1000 genomes]
rs970099	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1053466	chr12:51350285-51375969	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17125137	SCN8A	cis	cerebellum	SCAN
rs17125137	LASS5	cis	parietal	SCAN
rs17125137	CELA1	cis	parietal	SCAN
rs17125137	TFCP2	cis	cerebellum	SCAN
rs17125137	CSRNP2	cis	cerebellum	SCAN
rs17125137	DDN	cis	cerebellum	SCAN
rs17125137	KRT79	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
2	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
3	chr12:51329600-51373600	Weak transcription	Left Ventricle	heart
4	chr12:51331400-51378400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:51331600-51373800	Weak transcription	Pancreas	Pancrea
6	chr12:51331800-51382000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:51331800-51382000	Weak transcription	Ovary	ovary
8	chr12:51341600-51378200	Weak transcription	Right Ventricle	heart
9	chr12:51341800-51372600	Weak transcription	Osteobl	bone
10	chr12:51341800-51383200	Weak transcription	Fetal Brain Male	brain
11	chr12:51342400-51373200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:51342800-51378400	Weak transcription	NHLF	lung
13	chr12:51343000-51366200	Weak transcription	Brain Germinal Matrix	brain
14	chr12:51343600-51366200	Weak transcription	Gastric	stomach
15	chr12:51344000-51382000	Weak transcription	Esophagus	oesophagus
16	chr12:51344600-51381600	Weak transcription	Spleen	Spleen
17	chr12:51347200-51378000	Weak transcription	Brain Angular Gyrus	brain
18	chr12:51347400-51378000	Weak transcription	Brain Anterior Caudate	brain
19	chr12:51350800-51380600	Weak transcription	Fetal Lung	lung
20	chr12:51351200-51365200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:51354200-51365200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:51354400-51365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:51354400-51365200	Weak transcription	Dnd41	blood
24	chr12:51354400-51383800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:51355200-51365200	Weak transcription	HSMM	muscle
26	chr12:51355600-51378000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:51355800-51366200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:51355800-51378000	Weak transcription	A549	lung
29	chr12:51356000-51365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:51356000-51372600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:51357600-51378000	Weak transcription	Psoas Muscle	Psoas
32	chr12:51358200-51366200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:51358400-51365200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:51358800-51377800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:51359600-51365200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:51359800-51380400	Weak transcription	Fetal Kidney	kidney
37	chr12:51360000-51366400	Strong transcription	Fetal Thymus	thymus
38	chr12:51360200-51365600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:51360200-51374400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr12:51360200-51381800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:51360400-51365200	Weak transcription	Liver	Liver
42	chr12:51360400-51365800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:51360400-51372600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:51360400-51374400	Weak transcription	HUVEC	blood vessel
45	chr12:51360600-51365200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:51360600-51381000	Weak transcription	Primary B cells from cord blood	blood
47	chr12:51360600-51381800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:51361600-51365400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:51361600-51382200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:51361800-51365800	Weak transcription	H1 Cell Line	embryonic stem cell

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