Variant report

Variant	rs7029844
Chromosome Location	chr9:117878911-117878912
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	POLR2A	chr9:117858058-117881674	U87	brain:	n/a	n/a
2	GATA3	chr9:117878850-117879494	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr9:117877891-117881556	U87	brain:	n/a	n/a
4	GATA3	chr9:117876789-117879555	SK-N-SH	brain:	n/a	chr9:117878767-117878775
5	POLR2A	chr9:117877249-117881760	IMR90	lung:	n/a	n/a
6	TCF12	chr9:117876852-117879384	SK-N-SH	brain:	n/a	chr9:117876898-117876905
7	POLR2A	chr9:117877221-117881586	U87	brain:	n/a	n/a
8	PBX3	chr9:117878210-117879371	SK-N-SH	brain:	n/a	n/a
9	EP300	chr9:117878851-117879073	SK-N-SH_RA	brain:	n/a	n/a
10	POLR2A	chr9:117877960-117879114	MCF10A-Er-Src	breast:	n/a	n/a
11	RCOR1	chr9:117877222-117879859	IMR90	lung:	n/a	n/a
12	EP300	chr9:117877875-117879433	SK-N-SH	brain:	n/a	chr9:117879156-117879172
13	SIN3AK20	chr9:117878780-117879124	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr9:117876174-117879494	SK-N-SH	brain:	n/a	chr9:117876898-117876905
15	EP300	chr9:117878766-117879134	SK-N-SH_RA	brain:	n/a	n/a
16	POLR2A	chr9:117876849-117879682	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr9:117863693-117881740	U87	brain:	n/a	n/a
18	NFIC	chr9:117876700-117879564	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1000109	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1000110	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1000111	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10759756	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10759757	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10817714	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10817715	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10817716	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10817718	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10982550	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10982557	0.92[ASN][1000 genomes]
rs10982572	0.85[ASN][1000 genomes]
rs10982576	0.83[ASN][1000 genomes]
rs10982598	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1111784	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11788578	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11792657	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11793679	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11794627	0.83[ASN][1000 genomes]
rs12376564	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12376870	0.88[ASN][1000 genomes]
rs12378459	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12379019	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12380363	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12554357	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12554651	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1360290	0.92[ASN][1000 genomes]
rs1411458	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16936516	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2001693	0.92[ASN][1000 genomes]
rs2012566	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2012775	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2900594	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3748166	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4448357	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4978620	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4979499	0.83[CEU][hapmap]
rs4979500	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4979501	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4979503	0.87[CEU][hapmap]
rs4979506	0.88[ASN][1000 genomes]
rs57814325	1.00[ASN][1000 genomes]
rs58134557	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58160054	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61508829	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62580502	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6478132	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7018653	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7021057	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7024048	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7025283	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7029482	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7035705	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7039636	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7039915	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7040521	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7849460	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7849467	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7850000	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7850007	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7858535	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7865971	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs884790	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117870400-117879000	Weak transcription	Esophagus	oesophagus
2	chr9:117875400-117879000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:117876000-117879400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:117876400-117880200	Enhancers	Hela-S3	cervix
5	chr9:117876600-117879000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
6	chr9:117876800-117879000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr9:117876800-117879200	Enhancers	HSMM	muscle
8	chr9:117877000-117879400	Flanking Active TSS	NH-A	brain
9	chr9:117877200-117881400	Active TSS	Fetal Kidney	kidney
10	chr9:117877400-117879400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:117877400-117879800	Flanking Active TSS	Osteobl	bone
12	chr9:117877600-117879000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr9:117877600-117879800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:117877600-117880200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr9:117877600-117881600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
16	chr9:117877800-117879200	Flanking Active TSS	NHDF-Ad	bronchial
17	chr9:117877800-117879600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
18	chr9:117877800-117880000	Active TSS	Fetal Brain Female	brain
19	chr9:117878000-117880200	Active TSS	Stomach Smooth Muscle	stomach
20	chr9:117878000-117881600	Active TSS	Colon Smooth Muscle	Colon
21	chr9:117878200-117880200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:117878200-117880400	Active TSS	Rectal Smooth Muscle	rectum
23	chr9:117878200-117880800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:117878200-117881000	Active TSS	NHLF	lung
25	chr9:117878200-117881400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:117878200-117881600	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr9:117878200-117881600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr9:117878400-117879000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
29	chr9:117878400-117879200	Enhancers	Fetal Lung	lung
30	chr9:117878400-117879800	Flanking Active TSS	HMEC	breast
31	chr9:117878400-117880000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:117878400-117880200	Active TSS	Brain Germinal Matrix	brain
33	chr9:117878400-117880600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:117878400-117881000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr9:117878600-117879200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
36	chr9:117878600-117879800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:117878600-117879800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
38	chr9:117878600-117879800	Flanking Active TSS	NHEK	skin
39	chr9:117878600-117880000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:117878600-117880000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:117878600-117880200	Active TSS	Brain Anterior Caudate	brain
42	chr9:117878600-117880200	Bivalent/Poised TSS	Fetal Brain Male	brain
43	chr9:117878600-117880200	Active TSS	Fetal Muscle Trunk	muscle
44	chr9:117878600-117880400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:117878600-117880600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
46	chr9:117878600-117880600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
47	chr9:117878600-117881400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:117878600-117881400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:117878800-117879000	Enhancers	Aorta	Aorta
50	chr9:117878800-117879400	Active TSS	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links