Variant report

Variant	rs7965566
Chromosome Location	chr12:51331164-51331165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51325095..51327824-chr12:51330132..51332828,3	K562	blood:
2	chr12:51325095..51328187-chr12:51330132..51332748,3	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1005559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1048230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10506298	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10506299	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169626	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169633	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169636	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169637	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169639	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169641	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169644	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169646	0.85[ASN][1000 genomes]
rs11169647	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169648	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169649	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169655	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169661	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169667	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169669	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169670	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169671	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169672	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169682	0.87[CEU][hapmap]
rs11519977	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11831810	0.84[CEU][hapmap]
rs11831946	0.85[CEU][hapmap]
rs11833022	0.87[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap]
rs12366476	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366756	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12369278	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369658	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369666	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371463	0.86[EUR][1000 genomes]
rs12372173	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12809563	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810659	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12811508	0.81[CEU][hapmap]
rs12811684	0.81[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap]
rs12811777	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812727	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813728	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12817386	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12818033	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819296	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821444	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12824840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12824958	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826153	0.91[GIH][hapmap];0.85[TSI][hapmap]
rs12827861	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12828536	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12830048	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12830073	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12830422	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12831269	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12831597	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs15897	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17125137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17296192	0.81[CEU][hapmap]
rs224565	0.87[ASN][1000 genomes]
rs224589	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs224591	0.85[ASN][1000 genomes]
rs2285228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2285230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2516742	0.83[ASN][1000 genomes]
rs2630364	0.86[ASN][1000 genomes]
rs319932	0.87[ASN][1000 genomes]
rs34514224	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35037088	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35262273	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35379220	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35656976	0.83[ASN][1000 genomes]
rs35999440	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407135	0.85[ASN][1000 genomes]
rs422637	0.83[ASN][1000 genomes]
rs422982	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs440595	0.81[ASN][1000 genomes]
rs4444142	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4471501	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs454520	0.85[ASN][1000 genomes]
rs4768967	0.80[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]
rs6580784	0.81[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap]
rs6580792	0.81[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]
rs6580793	0.81[CEU][hapmap]
rs67025973	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67133203	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67259551	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs706801	0.90[ASN][1000 genomes]
rs706802	0.90[ASN][1000 genomes]
rs71445768	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71445772	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7305638	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306293	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090655	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954140	0.81[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]
rs7959075	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959082	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972406	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7975147	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7978723	0.87[CEU][hapmap];0.88[GIH][hapmap]
rs829022	0.90[ASN][1000 genomes]
rs853235	0.82[JPT][hapmap]

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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7965566	SCN8A	cis	cerebellum	SCAN
rs7965566	CSRNP2	cis	cerebellum	SCAN
rs7965566	LASS5	cis	parietal	SCAN
rs7965566	DDN	cis	cerebellum	SCAN
rs7965566	TFCP2	cis	cerebellum	SCAN
rs7965566	CELA1	cis	parietal	SCAN
rs7965566	KRT79	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51319400-51346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51322200-51332600	Weak transcription	Fetal Kidney	kidney
3	chr12:51322800-51331800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
5	chr12:51324200-51331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:51324400-51331200	Enhancers	Stomach Mucosa	stomach
7	chr12:51327200-51331400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr12:51327400-51331400	Weak transcription	Colonic Mucosa	Colon
9	chr12:51327400-51331400	Enhancers	Placenta	Placenta
10	chr12:51327600-51331400	Weak transcription	Brain Angular Gyrus	brain
11	chr12:51327800-51331200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:51327800-51331200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:51328000-51331200	Weak transcription	Fetal Lung	lung
14	chr12:51328400-51332600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
16	chr12:51329000-51331200	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:51329200-51331200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr12:51329200-51331400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:51329200-51331400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:51329200-51336200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:51329200-51341600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:51329400-51331200	Weak transcription	HSMMtube	muscle
23	chr12:51329400-51331400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:51329600-51331400	Weak transcription	Ovary	ovary
25	chr12:51329600-51331600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:51329600-51333200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:51329600-51373600	Weak transcription	Left Ventricle	heart
28	chr12:51330200-51331600	Enhancers	K562	blood
29	chr12:51330400-51331200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:51330400-51331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:51330400-51331400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr12:51330400-51331600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:51330400-51332600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
34	chr12:51330600-51331400	Enhancers	Colon Smooth Muscle	Colon
35	chr12:51330600-51332800	Weak transcription	Liver	Liver
36	chr12:51330800-51331200	Enhancers	HMEC	breast
37	chr12:51330800-51331800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr12:51330800-51331800	Strong transcription	Brain Hippocampus Middle	brain
39	chr12:51330800-51332000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr12:51330800-51332200	ZNF genes & repeats	Fetal Thymus	thymus
41	chr12:51330800-51332400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:51330800-51332400	ZNF genes & repeats	Brain Germinal Matrix	brain
43	chr12:51330800-51332400	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr12:51330800-51332400	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr12:51330800-51332600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
46	chr12:51330800-51332600	ZNF genes & repeats	Fetal Brain Female	brain
47	chr12:51331000-51331200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:51331000-51331200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:51331000-51331200	Strong transcription	Brain Anterior Caudate	brain
50	chr12:51331000-51331200	Enhancers	Right Atrium	heart

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