Variant report

Variant	rs2274835
Chromosome Location	chr9:117838624-117838625
allele	C/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	chr9:117837912-117838968	U87	brain:	n/a	n/a
2	REST	chr9:117838535-117839146	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr9:117837891-117839037	U87	brain:	n/a	n/a
4	POLR2A	chr9:117838519-117838805	ECC-1	luminal epithelium:	n/a	n/a
5	REST	chr9:117838548-117839212	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10817710	0.90[CEU][hapmap]
rs10982497	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs10982503	0.94[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs10982504	0.82[ASN][1000 genomes]
rs10982509	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10982516	0.90[CEU][hapmap]
rs11788513	0.83[ASN][1000 genomes]
rs12235159	0.90[CEU][hapmap]
rs12338715	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12340324	0.90[CEU][hapmap]
rs12343737	0.89[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12344929	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12346640	0.88[CEU][hapmap]
rs12347433	0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12348090	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12349585	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13285041	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1411453	0.89[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1411455	0.89[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2274751	0.81[AFR][1000 genomes]
rs2297179	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297181	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28491824	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34865477	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789871	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3789875	0.93[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs4394462	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66539628	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7030384	0.89[CEU][hapmap]
rs7859478	0.89[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
3	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117817800-117850600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:117819800-117848000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:117821400-117840200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:117822400-117854400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:117825400-117848000	Weak transcription	Lung	lung
9	chr9:117826800-117849400	Strong transcription	Osteobl	bone
10	chr9:117827000-117848600	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:117827000-117849200	Strong transcription	NHDF-Ad	bronchial
12	chr9:117827200-117855200	Strong transcription	NH-A	brain
13	chr9:117827400-117849200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:117829400-117839200	Strong transcription	NHLF	lung
15	chr9:117830400-117840800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:117831800-117848000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr9:117832400-117840600	Strong transcription	Fetal Stomach	stomach
18	chr9:117832400-117842400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:117832600-117839000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:117833800-117840400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:117834000-117849400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:117834000-117849800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:117834200-117840400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr9:117834200-117842000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:117834400-117839000	Strong transcription	Fetal Muscle Leg	muscle
26	chr9:117834600-117839000	Strong transcription	Colon Smooth Muscle	Colon
27	chr9:117834800-117840600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:117834800-117848600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr9:117835000-117840200	Weak transcription	Fetal Kidney	kidney
30	chr9:117835000-117842400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr9:117835200-117840400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:117835800-117839000	Strong transcription	Fetal Lung	lung
33	chr9:117835800-117841800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:117836000-117848600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:117836200-117839000	Strong transcription	NHEK	skin
36	chr9:117836200-117839600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:117836400-117839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:117837000-117838800	Strong transcription	HMEC	breast
39	chr9:117837000-117839000	Strong transcription	Rectal Smooth Muscle	rectum
40	chr9:117837000-117844400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:117837000-117849400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:117838200-117839000	Strong transcription	Aorta	Aorta
43	chr9:117838200-117839000	Strong transcription	Fetal Intestine Large	intestine
44	chr9:117838400-117839200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:117838600-117838800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:117838600-117839000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:117838600-117839000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr9:117838600-117839000	ZNF genes & repeats	Esophagus	oesophagus
49	chr9:117838600-117840200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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