Variant report

Variant	rs2070178
Chromosome Location	chr3:121361787-121361788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10934555	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128154	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1128158	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11927625	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1492178	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2141488	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2331812	0.85[EUR][1000 genomes]
rs3772129	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3966068	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438644	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6770842	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6804322	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179962	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73179967	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356043	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818194	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818402	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846174	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859243	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9873644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883663	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2070178	HCLS1	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 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	chr3:121347200-121364400	Strong transcription	Primary B cells from cord blood	blood
4	chr3:121347400-121367200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:121347600-121364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:121347600-121364600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:121347600-121364600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:121347800-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:121348000-121364600	Strong transcription	Primary B cells from peripheral blood	blood
10	chr3:121348000-121364600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr3:121348000-121381800	Weak transcription	Aorta	Aorta
12	chr3:121348200-121364600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:121348400-121364600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:121348400-121364600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:121348800-121363000	Weak transcription	Left Ventricle	heart
16	chr3:121348800-121364400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:121348800-121367200	Weak transcription	Pancreas	Pancrea
18	chr3:121349000-121364600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:121349000-121364600	Strong transcription	Dnd41	blood
20	chr3:121349000-121378000	Weak transcription	Fetal Stomach	stomach
21	chr3:121349200-121362000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:121349200-121364200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:121349400-121364600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:121349400-121367000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:121349600-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:121349800-121367000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:121350000-121364600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:121350000-121364600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:121351000-121364600	Strong transcription	GM12878-XiMat	blood
30	chr3:121351000-121382800	Weak transcription	Small Intestine	intestine
31	chr3:121351400-121381400	Weak transcription	Gastric	stomach
32	chr3:121351800-121370400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:121353400-121364400	Strong transcription	Fetal Thymus	thymus
34	chr3:121353400-121376000	Weak transcription	Lung	lung
35	chr3:121354000-121381000	Weak transcription	Fetal Intestine Small	intestine
36	chr3:121355600-121367000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:121356000-121370200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:121356200-121378200	Weak transcription	Colonic Mucosa	Colon
39	chr3:121356800-121362000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:121356800-121379200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:121357600-121362200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:121358000-121361800	Weak transcription	HUVEC	blood vessel
43	chr3:121358800-121361800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:121360000-121362400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:121360200-121364200	Strong transcription	Adipose Nuclei	Adipose
46	chr3:121360200-121364600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:121360200-121364600	Strong transcription	Placenta	Placenta
48	chr3:121360600-121364600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:121361200-121364600	Strong transcription	Primary T cells from cord blood	blood
50	chr3:121361200-121364600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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