Variant report

Variant	rs12369858
Chromosome Location	chr12:122843004-122843005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10734915	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs10734924	0.88[JPT][hapmap];0.80[TSI][hapmap]
rs10744211	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs10773075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap]
rs10773088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10773103	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs10773152	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs10773208	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs10846664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs10846688	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10846699	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs10846746	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10846921	0.94[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs10846978	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs10847179	0.88[JPT][hapmap]
rs10998	0.87[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs11058226	0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs11058402	0.88[JPT][hapmap]
rs12372756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1473553	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap]
rs1803290	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1973463	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2062488	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs2341439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs3817011	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs4758643	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs4758648	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs4758662	0.86[YRI][hapmap]
rs4758666	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs4997380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs6488958	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs7294559	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]
rs7301515	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs7314638	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs7956480	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap]
rs7964138	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs7975747	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs9988963	0.87[CHD][hapmap];0.88[JPT][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12369858	GTF2H3	cis	cerebellum	SCAN
rs12369858	NME2P1	cis	cerebellum	SCAN
rs12369858	RNF34	cis	parietal	SCAN
rs12369858	B3GNT4	cis	cerebellum	SCAN
rs12369858	GATC	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122812800-122844000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:122812800-122850600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:122818400-122852800	Weak transcription	Stomach Mucosa	stomach
4	chr12:122818600-122844200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:122834400-122845400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:122837000-122851200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:122837600-122856000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:122838000-122868000	Weak transcription	Fetal Lung	lung
9	chr12:122838600-122852200	Weak transcription	Small Intestine	intestine
10	chr12:122839400-122850200	Weak transcription	Right Atrium	heart
11	chr12:122839600-122844000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:122839600-122851400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:122839600-122861800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:122839600-122871000	Weak transcription	Fetal Kidney	kidney
15	chr12:122839800-122843400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:122839800-122843800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:122839800-122843800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:122839800-122843800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:122839800-122844000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:122840000-122843400	Weak transcription	Left Ventricle	heart
21	chr12:122840000-122843400	Weak transcription	Ovary	ovary
22	chr12:122840000-122843400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:122840000-122843800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:122840000-122843800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:122840000-122843800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:122840000-122843800	Weak transcription	GM12878-XiMat	blood
27	chr12:122840000-122844000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:122840000-122844000	Weak transcription	Adipose Nuclei	Adipose
29	chr12:122840000-122844000	Weak transcription	Brain Anterior Caudate	brain
30	chr12:122840000-122844000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:122840000-122844000	Weak transcription	Fetal Brain Female	brain
32	chr12:122840000-122844000	Weak transcription	Fetal Thymus	thymus
33	chr12:122840000-122844000	Weak transcription	Right Ventricle	heart
34	chr12:122840000-122844200	Weak transcription	Thymus	Thymus
35	chr12:122840000-122844800	Weak transcription	Colonic Mucosa	Colon
36	chr12:122840000-122845200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:122840000-122845400	Weak transcription	Psoas Muscle	Psoas
38	chr12:122840000-122852000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:122840000-122861800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:122840000-122862600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:122840200-122845400	Weak transcription	Aorta	Aorta
42	chr12:122840200-122851000	Weak transcription	NH-A	brain
43	chr12:122840200-122857800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:122840400-122843200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:122840400-122844200	Weak transcription	Spleen	Spleen
46	chr12:122840600-122843400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:122840600-122843400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:122840600-122843400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:122840600-122843800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr12:122840600-122843800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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