Variant report

Variant	rs3966068
Chromosome Location	chr3:121372729-121372730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10934555	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128154	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1128158	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]
rs11927625	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12636562	0.81[YRI][hapmap]
rs1492178	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2070178	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141488	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2331812	0.85[EUR][1000 genomes]
rs3772129	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6438644	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6770842	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6804322	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179962	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73179967	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356043	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643293	0.81[YRI][hapmap]
rs9818194	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818402	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846174	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859243	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9873644	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873648	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883663	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968051	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
7	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS 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	39 gene(s)	inside rSNPs	diseases
8	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3966068	HCLS1	cis	Lymphoblastoid	GTEx
rs3966068	GOLGB1	cis	Temporal Cortex	GTEx
rs3966068	HCLS1	cis	multi-tissue	Pritchard
rs3966068	GOLGB1	cis	Cerebellum	GTEx
rs3966068	GOLGB1	cis	Brain Pons	GTEx
rs3966068	GOLGB1	cis	uninvolved skin	skin_eQTL
rs3966068	GOLGB1	cis	Frontal Cortex	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121345600-121376800	Weak transcription	Esophagus	oesophagus
2	chr3:121347000-121378000	Weak transcription	Right Ventricle	heart
3	chr3:121348000-121381800	Weak transcription	Aorta	Aorta
4	chr3:121349000-121378000	Weak transcription	Fetal Stomach	stomach
5	chr3:121351000-121382800	Weak transcription	Small Intestine	intestine
6	chr3:121351400-121381400	Weak transcription	Gastric	stomach
7	chr3:121353400-121376000	Weak transcription	Lung	lung
8	chr3:121354000-121381000	Weak transcription	Fetal Intestine Small	intestine
9	chr3:121356200-121378200	Weak transcription	Colonic Mucosa	Colon
10	chr3:121356800-121379200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:121362200-121379400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:121362600-121379600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:121364000-121377000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:121364200-121373600	Weak transcription	Thymus	Thymus
15	chr3:121364200-121375800	Weak transcription	Spleen	Spleen
16	chr3:121364200-121377000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:121364200-121378200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:121364200-121378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:121366000-121373400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:121366200-121373400	Strong transcription	Primary B cells from cord blood	blood
21	chr3:121366200-121373600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:121366200-121373600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:121366800-121373400	Strong transcription	Primary hematopoietic stem cells	blood
24	chr3:121367400-121379000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:121367400-121381800	Weak transcription	Pancreas	Pancrea
26	chr3:121367600-121373600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr3:121367600-121377600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:121367600-121378000	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:121367600-121378200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:121367600-121378800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:121367800-121375000	Weak transcription	Adipose Nuclei	Adipose
32	chr3:121367800-121378800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:121368400-121377600	Weak transcription	Left Ventricle	heart
34	chr3:121368800-121380000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:121369000-121373600	Strong transcription	Fetal Thymus	thymus
36	chr3:121369400-121376200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:121369600-121375000	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr3:121369800-121377600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:121370600-121373600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:121370600-121379400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:121370600-121381600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:121370800-121373000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:121371000-121373400	Weak transcription	HUVEC	blood vessel
44	chr3:121371000-121383600	Weak transcription	Hela-S3	cervix
45	chr3:121371400-121378200	Weak transcription	Brain Anterior Caudate	brain
46	chr3:121371600-121373200	Strong transcription	Dnd41	blood
47	chr3:121371600-121374600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr3:121371600-121376200	Strong transcription	Placenta	Placenta
49	chr3:121371800-121373600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr3:121371800-121378000	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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