Variant report

Variant	rs10975512
Chromosome Location	chr9:6243819-6243820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10118795	0.97[ASN][1000 genomes]
rs10435816	0.82[EUR][1000 genomes]
rs10758750	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10815377	0.82[EUR][1000 genomes]
rs10815378	0.82[EUR][1000 genomes]
rs10815379	0.92[EUR][1000 genomes]
rs10815380	0.94[EUR][1000 genomes]
rs10815381	0.94[EUR][1000 genomes]
rs10815383	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10815388	0.90[ASN][1000 genomes]
rs10815390	0.95[ASN][1000 genomes]
rs10975497	0.80[EUR][1000 genomes]
rs10975498	0.81[EUR][1000 genomes]
rs10975499	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10975509	0.95[ASN][1000 genomes]
rs10975514	0.91[ASN][1000 genomes]
rs10975515	0.91[ASN][1000 genomes]
rs10975516	0.91[ASN][1000 genomes]
rs11792139	0.91[ASN][1000 genomes]
rs11792633	0.91[ASN][1000 genomes]
rs12341955	0.95[ASN][1000 genomes]
rs12351913	0.90[ASN][1000 genomes]
rs12551256	0.90[ASN][1000 genomes]
rs12683567	0.90[ASN][1000 genomes]
rs1317230	0.91[ASN][1000 genomes]
rs1330383	0.91[ASN][1000 genomes]
rs1375	0.96[ASN][1000 genomes]
rs1418385	0.82[EUR][1000 genomes]
rs1418386	0.82[EUR][1000 genomes]
rs16924171	0.90[ASN][1000 genomes]
rs1929992	0.91[ASN][1000 genomes]
rs2026990	0.82[EUR][1000 genomes]
rs2210463	0.82[EUR][1000 genomes]
rs2210464	0.92[EUR][1000 genomes]
rs4237163	0.95[ASN][1000 genomes]
rs4237164	0.95[ASN][1000 genomes]
rs4740840	0.81[EUR][1000 genomes]
rs4742170	0.98[ASN][1000 genomes]
rs7019575	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7025417	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7033258	0.96[ASN][1000 genomes]
rs7034720	0.94[ASN][1000 genomes]
rs7849201	0.91[ASN][1000 genomes]
rs928414	0.96[ASN][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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6229400-6251000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:6234600-6246400	Weak transcription	Ovary	ovary
3	chr9:6237200-6258400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:6238600-6252400	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:6239400-6255200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:6239400-6257600	Weak transcription	Brain Anterior Caudate	brain
7	chr9:6239600-6247800	Weak transcription	Fetal Intestine Large	intestine
8	chr9:6239800-6246400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:6239800-6251600	Weak transcription	Gastric	stomach
10	chr9:6240200-6244000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:6242000-6247600	Weak transcription	Stomach Mucosa	stomach
12	chr9:6243000-6244800	Strong transcription	Stomach Smooth Muscle	stomach
13	chr9:6243000-6246400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr9:6243200-6244000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:6243200-6250600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:6243200-6255800	Weak transcription	Left Ventricle	heart
17	chr9:6243400-6256200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:6243600-6244200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:6243600-6244200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr9:6243600-6244200	Enhancers	NHEK	skin
21	chr9:6243600-6244400	Enhancers	Osteobl	bone
22	chr9:6243600-6244800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:6243600-6245000	Enhancers	HMEC	breast
24	chr9:6243800-6244000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr9:6243800-6244200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:6243800-6244200	Flanking Active TSS	GM12878-XiMat	blood
27	chr9:6243800-6244200	Enhancers	HepG2	liver

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