Variant report

Variant	rs17767994
Chromosome Location	chr2:46860079-46860080
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46858190..46860750-chr2:46875566..46879072,3	MCF-7	breast:
2	chr2:46857941..46860814-chr2:46872610..46874404,2	MCF-7	breast:
3	chr2:46859234..46860222-chr2:46877710..46878290,6	MCF-7	breast:
4	chr2:46859576..46860085-chr2:47115905..47116595,2	MCF-7	breast:
5	chr2:46859559..46860170-chr2:47103480..47104015,2	MCF-7	breast:
6	chr2:46859579..46860115-chr2:46996827..46997682,2	MCF-7	breast:
7	chr2:46859166..46860148-chr2:47003282..47004503,4	K562	blood:
8	chr2:46859268..46860339-chr2:46877395..46878304,7	MCF-7	breast:

No data

Extended variants
information (count: 47 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10495935	0.81[JPT][hapmap]
rs12105006	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13013245	0.90[JPT][hapmap]
rs13024534	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032670	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13033177	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13406427	0.84[ASN][1000 genomes]
rs13417558	0.84[ASN][1000 genomes]
rs1378764	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17035488	0.81[JPT][hapmap]
rs17768018	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768132	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768138	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17768226	0.86[ASN][1000 genomes]
rs17819022	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1824050	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2122715	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34449783	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748737	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34752561	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34996358	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35350086	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35449212	0.93[ASN][1000 genomes]
rs35682608	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35837037	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35909669	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35949012	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952837	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55742873	0.86[ASN][1000 genomes]
rs62136873	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136894	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62136895	0.82[ASN][1000 genomes]
rs62136898	0.84[ASN][1000 genomes]
rs6746598	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565274	0.95[ASN][1000 genomes]
rs7605089	0.84[ASN][1000 genomes]
rs896212	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	esv3395825	chr2:46859884-46860292	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs17767994	CRIPT	cis	brain	seeQTL
rs17767994	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs17767994	CRIPT	cis	Temporal Cortex	GTEx
rs17767994	ATP6V1E2	cis	brain	seeQTL
rs17767994	PIGF	cis	cerebellum	SCAN
rs17767994	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs17767994	ATP6V1E2	cis	multi-tissue	Pritchard
rs17767994	PIGF	cis	parietal	SCAN
rs17767994	CRIPT	cis	Frontal Cortex	GTEx
rs17767994	CRIPT	cis	Artery Tibial	GTEx
rs17767994	CRIPT	cis	lymphoblastoid	seeQTL
rs17767994	PIGF	cis	lymphoblastoid	seeQTL
rs17767994	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs17767994	CRIPT	cis	multi-tissue	Pritchard
rs17767994	ATP6V1E2	cis	parietal	SCAN
rs17767994	CRIPT	cis	parietal	SCAN
rs17767994	SOCS5	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46844800-46865600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:46844800-46868400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:46844800-46868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:46844800-46868800	Weak transcription	Esophagus	oesophagus
5	chr2:46844800-46872200	Weak transcription	Pancreas	Pancrea
6	chr2:46845400-46864800	Weak transcription	Psoas Muscle	Psoas
7	chr2:46845400-46867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:46845400-46871000	Weak transcription	Stomach Mucosa	stomach
9	chr2:46845400-46873000	Weak transcription	Right Ventricle	heart
10	chr2:46845600-46868200	Weak transcription	Aorta	Aorta
11	chr2:46845600-46868800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:46846000-46868600	Weak transcription	Fetal Intestine Small	intestine
13	chr2:46848600-46860600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:46848600-46861800	Weak transcription	GM12878-XiMat	blood
15	chr2:46848600-46864800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:46848600-46867400	Weak transcription	Lung	lung
17	chr2:46848600-46871200	Weak transcription	HSMMtube	muscle
18	chr2:46848600-46872600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:46848600-46872800	Weak transcription	Left Ventricle	heart
20	chr2:46848600-46872800	Weak transcription	Ovary	ovary
21	chr2:46848800-46868000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:46848800-46871000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:46848800-46872600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:46848800-46873000	Weak transcription	Brain Angular Gyrus	brain
25	chr2:46849000-46861800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:46849000-46868600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:46849000-46868600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:46849000-46877200	Weak transcription	Brain Substantia Nigra	brain
29	chr2:46849200-46861600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:46849200-46869400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:46849200-46869800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:46849200-46870800	Weak transcription	Hela-S3	cervix
33	chr2:46849200-46872600	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:46849400-46872800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:46849800-46868200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:46850200-46868400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:46851000-46861600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:46851000-46861800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:46851600-46867600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:46852000-46861800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:46852000-46868200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:46852000-46872800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:46852400-46869400	Weak transcription	Dnd41	blood
44	chr2:46853400-46865600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:46853400-46869600	Weak transcription	Brain Germinal Matrix	brain
46	chr2:46853400-46872600	Weak transcription	Brain Anterior Caudate	brain
47	chr2:46853400-46872800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:46853600-46862000	Weak transcription	HepG2	liver
49	chr2:46853600-46868600	Weak transcription	Fetal Intestine Large	intestine
50	chr2:46853600-46869400	Weak transcription	NH-A	brain

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