Variant report

Variant	rs4740840
Chromosome Location	chr9:6229110-6229111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10118795	0.90[GIH][hapmap];0.86[JPT][hapmap]
rs10435816	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758750	0.90[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10815377	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10815378	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10815379	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10815380	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10815381	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10815383	0.90[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10815388	0.90[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs10975497	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10975498	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10975499	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10975509	0.81[JPT][hapmap]
rs10975512	0.81[EUR][1000 genomes]
rs12551256	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1330383	0.82[JPT][hapmap]
rs1375	0.81[JPT][hapmap]
rs1418385	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1418386	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16924171	0.86[JPT][hapmap]
rs1929992	0.82[JPT][hapmap]
rs2026990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2210463	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];0.86[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2210464	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4237164	0.81[JPT][hapmap]
rs4742170	0.90[GIH][hapmap];0.91[JPT][hapmap]
rs7019575	0.91[JPT][hapmap]
rs7025417	0.86[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs7033258	0.90[GIH][hapmap];0.81[JPT][hapmap]
rs7034720	0.81[JPT][hapmap]
rs7044343	0.80[JPT][hapmap]
rs928414	0.90[GIH][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv613205	chr9:6032924-6332901	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv916394	chr9:6055497-6322471	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv892157	chr9:6093790-6322415	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv831496	chr9:6101763-6285088	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv521598	chr9:6142157-6291125	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv892158	chr9:6149006-6266440	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1027270	chr9:6152434-6328227	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv539968	chr9:6152434-6328227	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
14	nsv892159	chr9:6190076-6231239	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
16	esv2761483	chr9:6216925-6246144	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
18	nsv1019912	chr9:6224906-6257395	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv968563	chr9:6225006-6233899	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6218600-6232600	Weak transcription	Aorta	Aorta
2	chr9:6224800-6232600	Weak transcription	Brain Anterior Caudate	brain
3	chr9:6224800-6242800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:6225000-6229200	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:6225000-6230400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:6226400-6229200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:6226800-6230200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:6226800-6230200	Enhancers	Hela-S3	cervix
9	chr9:6227000-6241600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:6227200-6229200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:6227200-6230000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:6227200-6230000	Weak transcription	NH-A	brain
13	chr9:6227400-6229400	Weak transcription	HMEC	breast
14	chr9:6227400-6229600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:6227400-6230000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:6227400-6230200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:6227400-6231200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:6227800-6229200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:6228000-6231400	Enhancers	Pancreas	Pancrea
20	chr9:6228600-6230800	Enhancers	Fetal Intestine Small	intestine
21	chr9:6228800-6230600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr9:6228800-6232000	Weak transcription	Lung	lung
23	chr9:6229000-6229400	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr9:6229000-6229400	Enhancers	Gastric	stomach
25	chr9:6229000-6229600	Enhancers	Right Atrium	heart
26	chr9:6229000-6229600	Enhancers	Small Intestine	intestine
27	chr9:6229000-6230000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:6229000-6230200	Enhancers	NHEK	skin
29	chr9:6229000-6230800	Enhancers	Fetal Intestine Large	intestine
30	chr9:6229000-6231000	Enhancers	HUVEC	blood vessel
31	chr9:6229000-6232800	Enhancers	Stomach Mucosa	stomach

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