Variant report

Variant	rs2139198
Chromosome Location	chr2:86007674-86007675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr2:86007633-86007772	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:86007629-86007679	BJ	skin:	n/a
2	chr2:86007629-86007679	Hela-S3	cervix:	n/a
3	chr2:86007629-86007679	HIPEpiC	eye:	n/a
4	chr2:86007629-86007679	SKMC	muscle:	n/a
5	chr2:86007629-86007679	RPTEC	kidney:	n/a
6	chr2:86007629-86007679	SK-N-SH_RA	brain:	n/a
7	chr2:86007629-86007679	PANC-1	pancreas:	n/a
8	chr2:86007629-86007679	HCM	heart:	n/a
9	chr2:86007629-86007679	NB4	blood:	n/a
10	chr2:86007629-86007679	BE2_C	brain:	n/a
11	chr2:86007629-86007679	T-47D	breast:	n/a
12	chr2:86007629-86007679	AoSMC	blood vessel:	n/a
13	chr2:86007629-86007679	ovcar-3	ovarian:	n/a
14	chr2:86007629-86007679	CMK	blood:	n/a
15	chr2:86007629-86007679	MCF10A-Er-Src	breast:	n/a
16	chr2:86007629-86007679	NHDF-neo	bronchial:	n/a
17	chr2:86007629-86007679	HEEpiC	esophagus:	n/a
18	chr2:86007629-86007679	AG09319	gingival:	n/a
19	chr2:86007629-86007679	SAEC	small airway:	n/a
20	chr2:86007629-86007679	HepG2	liver:	n/a
21	chr2:86007629-86007679	Hepatocyte	liver:	n/a
22	chr2:86007629-86007679	PrEC	prostate:	n/a
23	chr2:86007629-86007679	GM12891	blood:	n/a
24	chr2:86007629-86007679	HNPCEpiC	eye:	n/a
25	chr2:86007629-86007679	IMR90	lung:	fetal
26	chr2:86007629-86007679	HRPEpiC	eye:	n/a
27	chr2:86007629-86007679	GM12892	blood:	n/a
28	chr2:86007629-86007679	AG04450	lung:	fetal
29	chr2:86007629-86007679	HEK293	kidney:	embryo
30	chr2:86007629-86007679	AG04449	skin:	fetal
31	chr2:86007629-86007679	HPAEpiC	pulmonary alveolar:	n/a
32	chr2:86007629-86007679	H1-hESC	embryonic stem cell:	embryo
33	chr2:86007629-86007679	LNCaP	prostate:	n/a
34	chr2:86007629-86007679	GM06990	blood:	n/a
35	chr2:86007629-86007679	HCPEpiC	choroid plexus:	n/a
36	chr2:86007629-86007679	NT2-D1	testis:	n/a
37	chr2:86007629-86007679	NH-A	brain:	n/a
38	chr2:86007629-86007679	HCT-116	colon:	n/a
39	chr2:86007629-86007679	MCF-7	breast:	n/a
40	chr2:86007629-86007679	GM12878	blood:	n/a
41	chr2:86007629-86007679	K562	blood:	n/a
42	chr2:86007629-86007679	GM19239	blood:	n/a
43	chr2:86007629-86007679	U87	brain:	n/a
44	chr2:86007629-86007679	HRCEpiC	kidney:	n/a
45	chr2:86007629-86007679	HAEpiC	amniotic membrane:	n/a
46	chr2:86007629-86007679	AG10803	skin:	n/a
47	chr2:86007629-86007679	Jurkat	blood:	n/a
48	chr2:86007629-86007679	AG09309	skin:	n/a
49	chr2:86007629-86007679	HRE	kidney:	n/a
50	chr2:86007629-86007679	ProgFib	skin:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86003504..86005582-chr2:86005800..86007921,2	K562	blood:

No data

Variant related genes	Relation type
ATOH8	TF binding region
ATOH8	CpG island

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10190632	0.85[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs10192235	0.93[ASN][1000 genomes]
rs10207516	0.97[EUR][1000 genomes]
rs13386681	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs13392366	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402783	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs13428557	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs1370545	0.83[CEU][hapmap]
rs1914821	0.86[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs2001593	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366818	0.86[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs3731826	0.97[EUR][1000 genomes]
rs55882144	0.83[EUR][1000 genomes]
rs727123	0.97[EUR][1000 genomes]
rs734042	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs869778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934775	0.85[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv874471	chr2:85976645-86021919	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1001792	chr2:85983107-86016722	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv535805	chr2:85983107-86016722	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv535806	chr2:85990408-86007918	Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86000200-86010400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:86000400-86008200	Enhancers	Psoas Muscle	Psoas
3	chr2:86000600-86009200	Enhancers	Right Atrium	heart
4	chr2:86001000-86008200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr2:86001200-86012800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:86001400-86023000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:86001600-86011800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:86001600-86020000	Weak transcription	Fetal Brain Female	brain
9	chr2:86001600-86023000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:86001800-86014200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:86002200-86008200	Genic enhancers	Stomach Smooth Muscle	stomach
12	chr2:86002200-86012600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:86002200-86015800	Weak transcription	A549	lung
14	chr2:86002400-86011200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:86002800-86008200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:86002800-86011800	Weak transcription	HSMMtube	muscle
17	chr2:86003000-86007800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:86003200-86007800	Genic enhancers	Lung	lung
19	chr2:86003400-86008600	Genic enhancers	Fetal Lung	lung
20	chr2:86003600-86008400	Genic enhancers	HSMM	muscle
21	chr2:86004000-86014000	Weak transcription	Gastric	stomach
22	chr2:86004800-86008000	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr2:86004800-86011000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:86004800-86017200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:86005000-86008600	Enhancers	Fetal Brain Male	brain
26	chr2:86005200-86007800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:86005200-86008000	Bivalent Enhancer	Fetal Stomach	stomach
28	chr2:86005400-86008000	Weak transcription	Osteobl	bone
29	chr2:86005400-86008200	Enhancers	Pancreas	Pancrea
30	chr2:86005400-86014400	Weak transcription	Fetal Intestine Large	intestine
31	chr2:86005400-86019200	Weak transcription	HUVEC	blood vessel
32	chr2:86005600-86008200	Enhancers	Colonic Mucosa	Colon
33	chr2:86005800-86008000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:86005800-86008200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr2:86005800-86008400	Genic enhancers	Right Ventricle	heart
36	chr2:86005800-86011200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:86005800-86011800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:86006000-86008000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:86006000-86008400	Enhancers	NHDF-Ad	bronchial
40	chr2:86006000-86011200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:86006000-86012000	Weak transcription	Fetal Heart	heart
42	chr2:86006200-86009000	Strong transcription	Fetal Intestine Small	intestine
43	chr2:86006400-86008600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:86006400-86008800	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr2:86006600-86007800	Genic enhancers	Brain Substantia Nigra	brain
46	chr2:86006600-86007800	Genic enhancers	Spleen	Spleen
47	chr2:86006600-86008200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:86006600-86008200	Genic enhancers	Left Ventricle	heart
49	chr2:86006600-86019000	Weak transcription	Esophagus	oesophagus
50	chr2:86006800-86020000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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