Variant report

Variant	rs1128158
Chromosome Location	chr3:121350593-121350594
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121344119..121346108-chr3:121348732..121350963,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10934555	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1128154	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[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]
rs11927625	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs1492178	0.92[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];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070178	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2141488	0.92[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];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2331812	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3966068	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6438644	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6770842	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.94[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];0.91[ASN][1000 genomes]
rs6804322	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73179962	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73179967	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7356043	0.92[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9818194	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9818402	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9846174	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9859243	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9873644	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9873648	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9883663	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers 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	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv999349	chr3:121253990-121360206	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1128158	GOLGB1	cis	Temporal Cortex	GTEx
rs1128158	HCLS1	cis	multi-tissue	Pritchard
rs1128158	IQCB1	cis	cerebellum	SCAN
rs1128158	HEG1	cis	parietal	SCAN
rs1128158	GOLGB1	cis	Brain Pons	GTEx
rs1128158	GOLGB1	cis	Cerebellum	GTEx
rs1128158	HCLS1	cis	lymphoblastoid	seeQTL
rs1128158	IQCB1	cis	parietal	SCAN
rs1128158	GOLGB1	cis	Frontal Cortex	GTEx
rs1128158	HCLS1	cis	Lymphoblastoid	GTEx
rs1128158	GOLGB1	cis	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121343800-121353000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:121345600-121376800	Weak transcription	Esophagus	oesophagus
3	chr3:121346200-121351600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:121346400-121351800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:121346400-121353200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:121346800-121351800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:121347000-121378000	Weak transcription	Right Ventricle	heart
8	chr3:121347200-121352600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:121347200-121364400	Strong transcription	Primary B cells from cord blood	blood
10	chr3:121347400-121350800	Weak transcription	Right Atrium	heart
11	chr3:121347400-121352200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:121347400-121367200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:121347600-121353000	Strong transcription	Fetal Thymus	thymus
14	chr3:121347600-121359400	Strong transcription	Primary T cells from cord blood	blood
15	chr3:121347600-121364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:121347600-121364600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:121347600-121364600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:121347800-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:121348000-121364600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:121348000-121364600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr3:121348000-121381800	Weak transcription	Aorta	Aorta
22	chr3:121348200-121364600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:121348400-121357400	Strong transcription	Spleen	Spleen
24	chr3:121348400-121364600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:121348400-121364600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr3:121348800-121358600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:121348800-121363000	Weak transcription	Left Ventricle	heart
28	chr3:121348800-121364400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:121348800-121367200	Weak transcription	Pancreas	Pancrea
30	chr3:121349000-121356600	Weak transcription	Brain Anterior Caudate	brain
31	chr3:121349000-121359000	Strong transcription	Primary hematopoietic stem cells	blood
32	chr3:121349000-121364600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:121349000-121364600	Strong transcription	Dnd41	blood
34	chr3:121349000-121378000	Weak transcription	Fetal Stomach	stomach
35	chr3:121349200-121351000	Genic enhancers	GM12878-XiMat	blood
36	chr3:121349200-121359200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:121349200-121362000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:121349200-121364200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:121349400-121364600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:121349400-121367000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:121349600-121358600	Strong transcription	Thymus	Thymus
42	chr3:121349600-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:121349800-121359400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:121349800-121367000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:121350000-121357400	Strong transcription	Liver	Liver
46	chr3:121350000-121364600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:121350000-121364600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:121350200-121350600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:121350200-121350800	Strong transcription	HUVEC	blood vessel
50	chr3:121350200-121351400	Strong transcription	Gastric	stomach

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