Variant report

Variant	rs16924161
Chromosome Location	chr9:6230912-6230913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10118795	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10435816	0.81[JPT][hapmap]
rs10758750	0.81[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10815383	0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10815388	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10975499	0.85[ASN][1000 genomes]
rs12351913	0.83[ASN][1000 genomes]
rs12551256	0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12683567	0.84[ASN][1000 genomes]
rs16924171	0.83[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2210464	0.82[MEX][hapmap]
rs4742170	0.86[JPT][hapmap]
rs7019575	0.86[JPT][hapmap]
rs7025417	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs7034720	0.82[CHB][hapmap]
rs7044343	0.80[JPT][hapmap]
rs7871381	0.84[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:30 , 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	chr9:6227000-6241600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:6227400-6231200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:6228000-6231400	Enhancers	Pancreas	Pancrea
7	chr9:6228800-6232000	Weak transcription	Lung	lung
8	chr9:6229000-6231000	Enhancers	HUVEC	blood vessel
9	chr9:6229000-6232800	Enhancers	Stomach Mucosa	stomach
10	chr9:6229200-6231400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:6229200-6231400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:6229400-6231200	Enhancers	HMEC	breast
13	chr9:6229400-6251000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:6229600-6231000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr9:6229600-6238200	Weak transcription	Right Atrium	heart
16	chr9:6230000-6231200	Enhancers	Small Intestine	intestine
17	chr9:6230400-6231400	Enhancers	Adipose Nuclei	Adipose
18	chr9:6230400-6238000	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:6230600-6231400	Enhancers	Gastric	stomach
20	chr9:6230600-6231800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr9:6230600-6237000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:6230600-6238800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:6230800-6231400	Enhancers	NHEK	skin
24	chr9:6230800-6231600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:6230800-6232000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:6230800-6232200	Enhancers	Hela-S3	cervix
27	chr9:6230800-6234400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:6230800-6238800	Weak transcription	Fetal Intestine Large	intestine
29	chr9:6230800-6239400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:6230800-6243000	Weak transcription	Stomach Smooth Muscle	stomach

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