Variant report

Variant	rs17498196
Chromosome Location	chr9:6237547-6237548
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10491836	0.91[GIH][hapmap]
rs10815392	0.93[EUR][1000 genomes]
rs10815393	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10975504	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10975507	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339348	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16924356	0.91[GIH][hapmap]
rs17582919	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7035413	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7038893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72689561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72689565	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
15	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
16	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
17	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

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6224800-6242800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:6227000-6241600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:6229400-6251000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:6229600-6238200	Weak transcription	Right Atrium	heart
5	chr9:6230400-6238000	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:6230600-6238800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:6230800-6238800	Weak transcription	Fetal Intestine Large	intestine
8	chr9:6230800-6239400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:6230800-6243000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:6231000-6239200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:6231600-6238600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:6234600-6239200	Weak transcription	Gastric	stomach
13	chr9:6234600-6242800	Weak transcription	Left Ventricle	heart
14	chr9:6234600-6246400	Weak transcription	Ovary	ovary
15	chr9:6236800-6240000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:6237000-6237600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:6237000-6237600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr9:6237000-6237600	Enhancers	Stomach Mucosa	stomach
19	chr9:6237000-6237600	Enhancers	Hela-S3	cervix
20	chr9:6237000-6237600	Enhancers	HMEC	breast
21	chr9:6237000-6238200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr9:6237000-6239600	Enhancers	Fetal Intestine Small	intestine
23	chr9:6237000-6239800	Enhancers	NHEK	skin
24	chr9:6237000-6240400	Enhancers	HepG2	liver
25	chr9:6237200-6238600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:6237200-6239200	Weak transcription	Brain Anterior Caudate	brain
27	chr9:6237200-6239200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:6237200-6258400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:6237400-6238400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:6237400-6238800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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