Variant report

Variant	rs9559794
Chromosome Location	chr13:111063799-111063800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr13:111063415-111065761	SK-N-SH	brain:	n/a	chr13:111063778-111063791 chr13:111063771-111063785 chr13:111063770-111063784
2	CHD1	chr13:111063393-111066220	IMR90	lung:	n/a	n/a
3	POLR2A	chr13:111063567-111065229	IMR90	lung:	n/a	n/a
4	KAP1	chr13:111063793-111065238	U2OS	brain:	n/a	chr13:111063939-111063947 chr13:111064668-111064677 chr13:111064671-111064680

Variant related genes	Relation type
ENSG00000238629	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10161705	0.86[MEX][hapmap]
rs10851243	0.86[MEX][hapmap]
rs12585289	0.85[CEU][hapmap]
rs12868443	0.86[MEX][hapmap]
rs1536622	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.93[ASN][1000 genomes]
rs4132949	0.90[JPT][hapmap]
rs4555010	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4773180	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61963204	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492270	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs9555696	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9555698	1.00[CEU][hapmap]
rs9559785	0.80[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs9559786	0.80[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs9559789	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9559790	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9559791	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9559792	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9559793	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs9588154	0.81[YRI][hapmap]
rs9588156	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2751128	chr13:111040798-111132490	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111050200-111064400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:111050200-111066000	Enhancers	NHDF-Ad	bronchial
3	chr13:111050200-111075200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:111056200-111066000	Enhancers	Lung	lung
5	chr13:111057800-111064800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr13:111057800-111070400	Enhancers	Right Atrium	heart
7	chr13:111058000-111066000	Enhancers	HUVEC	blood vessel
8	chr13:111058800-111063800	Weak transcription	Small Intestine	intestine
9	chr13:111058800-111064200	Weak transcription	Fetal Intestine Large	intestine
10	chr13:111059400-111063800	Genic enhancers	Fetal Stomach	stomach
11	chr13:111059400-111065200	Enhancers	Spleen	Spleen
12	chr13:111059400-111067000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr13:111059600-111064200	Genic enhancers	Osteobl	bone
14	chr13:111059600-111064400	Enhancers	Aorta	Aorta
15	chr13:111059800-111064800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:111059800-111065200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr13:111060200-111064000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:111060200-111064200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr13:111060200-111064200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr13:111060200-111064400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr13:111060200-111064400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr13:111060200-111065200	Enhancers	HMEC	breast
23	chr13:111060200-111065600	Weak transcription	Esophagus	oesophagus
24	chr13:111060200-111067000	Enhancers	Right Ventricle	heart
25	chr13:111060200-111082800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr13:111060400-111064000	Weak transcription	Brain Hippocampus Middle	brain
27	chr13:111060400-111064200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr13:111060400-111064400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr13:111060400-111064800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr13:111060800-111064000	Weak transcription	NHEK	skin
31	chr13:111061000-111065600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr13:111061000-111077000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr13:111061200-111064200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr13:111061200-111065800	Enhancers	Colon Smooth Muscle	Colon
35	chr13:111061400-111064800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:111061400-111065600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr13:111061400-111065600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr13:111061400-111065800	Enhancers	Rectal Smooth Muscle	rectum
39	chr13:111061600-111064000	Enhancers	Fetal Heart	heart
40	chr13:111061600-111064200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr13:111061600-111064200	Weak transcription	Pancreas	Pancrea
42	chr13:111061600-111065200	Enhancers	Fetal Kidney	kidney
43	chr13:111061600-111065800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr13:111061600-111069200	Weak transcription	Fetal Brain Male	brain
45	chr13:111061800-111064000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr13:111061800-111064400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr13:111061800-111064800	Enhancers	NH-A	brain
48	chr13:111061800-111066000	Enhancers	HSMM	muscle
49	chr13:111061800-111066200	Enhancers	NHLF	lung
50	chr13:111061800-111066800	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links