Variant report

Variant	rs7961258
Chromosome Location	chr12:122872750-122872751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10161184	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10161488	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744218	0.86[EUR][1000 genomes]
rs10744242	0.81[CHB][hapmap]
rs10773090	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10773108	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10773117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773162	0.86[EUR][1000 genomes]
rs10773230	0.81[CHB][hapmap];0.87[GIH][hapmap]
rs10846714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10846852	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10846871	0.86[ASN][1000 genomes]
rs10846912	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs10846968	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs11057514	0.87[EUR][1000 genomes]
rs11057522	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11057686	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11057705	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11057813	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11057819	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11058272	0.83[EUR][1000 genomes]
rs1129167	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11503023	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610303	0.81[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap]
rs11830957	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12308903	0.81[ASN][1000 genomes]
rs12314537	0.86[EUR][1000 genomes]
rs12812332	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs12817342	0.86[CHB][hapmap]
rs12818177	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12828876	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12829449	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1392142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1532579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1553178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2341438	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3825096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4356269	0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs4758657	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4758658	0.86[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs4758660	0.81[CHB][hapmap];0.84[GIH][hapmap]
rs4758664	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4758665	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4758692	0.86[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs4758693	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758695	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs61021925	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6416295	0.81[CHB][hapmap];0.84[GIH][hapmap]
rs6488947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6489014	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs6489051	0.81[CHB][hapmap]
rs6489056	0.87[GIH][hapmap]
rs7134381	0.81[CHB][hapmap]
rs7296680	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7298839	0.81[CHB][hapmap]
rs7305360	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7311573	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs7313121	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7313284	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7953204	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7955241	0.81[AMR][1000 genomes]
rs7955513	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs7959550	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7964981	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7970007	0.86[EUR][1000 genomes]
rs7972832	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7973480	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7974160	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7975492	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978119	0.86[EUR][1000 genomes]
rs7978636	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs868181	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9788228	0.95[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7961258	DYNLL1	cis	parietal	SCAN
rs7961258	NME2P1	cis	cerebellum	SCAN
rs7961258	DIABLO	cis	parietal	SCAN
rs7961258	CCDC62	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122846000-122883800	Weak transcription	Aorta	Aorta
2	chr12:122856400-122884200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:122856600-122877000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:122856600-122878200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:122860600-122905000	Weak transcription	Brain Germinal Matrix	brain
6	chr12:122862400-122876400	Weak transcription	Pancreas	Pancrea
7	chr12:122862400-122878600	Weak transcription	Primary B cells from cord blood	blood
8	chr12:122862400-122883800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:122862600-122873400	Weak transcription	NH-A	brain
10	chr12:122862600-122879400	Weak transcription	NHLF	lung
11	chr12:122862600-122881600	Weak transcription	Thymus	Thymus
12	chr12:122862600-122883800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:122862800-122895600	Weak transcription	Small Intestine	intestine
14	chr12:122863000-122876800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:122863000-122879400	Weak transcription	Osteobl	bone
16	chr12:122863000-122883600	Weak transcription	K562	blood
17	chr12:122863000-122883800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:122863200-122879400	Weak transcription	NHDF-Ad	bronchial
19	chr12:122863200-122883800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:122863400-122876600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr12:122863400-122883800	Weak transcription	Brain Anterior Caudate	brain
22	chr12:122863400-122884000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:122863400-122884200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:122863400-122884600	Weak transcription	Ovary	ovary
25	chr12:122863400-122897400	Weak transcription	Fetal Brain Female	brain
26	chr12:122863400-122897800	Weak transcription	Brain Substantia Nigra	brain
27	chr12:122863800-122873400	Weak transcription	NHEK	skin
28	chr12:122863800-122879600	Weak transcription	HMEC	breast
29	chr12:122863800-122883800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:122863800-122905000	Weak transcription	Dnd41	blood
31	chr12:122864000-122883800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:122864200-122873600	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:122864200-122884000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:122864400-122873600	Weak transcription	Left Ventricle	heart
35	chr12:122864400-122883800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:122865000-122877800	Weak transcription	Fetal Thymus	thymus
37	chr12:122865200-122873000	Weak transcription	Hela-S3	cervix
38	chr12:122865200-122876600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr12:122865200-122878000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:122865200-122879600	Weak transcription	HUVEC	blood vessel
41	chr12:122865200-122880800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:122865200-122883800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:122865200-122885000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:122865400-122879400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:122865400-122883800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:122866400-122883600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr12:122866600-122873200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:122866600-122876600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr12:122866600-122879200	Weak transcription	HepG2	liver
50	chr12:122866600-122879400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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