Variant report

Variant	rs1346311
Chromosome Location	chr2:231082387-231082388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IKZF1	chr2:231082166-231082492	GM12878	blood:	n/a	n/a
2	SPI1	chr2:231082181-231082528	GM12891	blood:	n/a	n/a
3	SPI1	chr2:231082108-231082904	GM12878	blood:	n/a	n/a
4	SPI1	chr2:231082223-231082508	GM12891	blood:	n/a	n/a
5	WRNIP1	chr2:231082343-231082685	GM12878	blood:	n/a	n/a
6	SPI1	chr2:231082198-231082456	GM12878	blood:	n/a	n/a
7	GATA3	chr2:231082088-231082512	T-47D	breast:	n/a	n/a
8	POLR2A	chr2:231082244-231082716	GM12878	blood:	n/a	n/a
9	SPI1	chr2:231082196-231082511	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:231082269-231082638	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:231072082..231074333-chr2:231080031..231082815,2	MCF-7	breast:
2	chr2:231080762..231082857-chr2:231083207..231085642,2	K562	blood:
3	chr2:231081815..231083756-chr2:231088866..231091364,2	MCF-7	breast:

No data

Variant related genes	Relation type
SP110	TF binding region
ENSG00000135899	Chromatin interaction
ENSG00000079263	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10164566	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs10177685	0.84[ASN][1000 genomes]
rs10200874	0.84[ASN][1000 genomes]
rs10498245	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10498250	1.00[CHB][hapmap]
rs10933332	1.00[CHB][hapmap]
rs10933333	1.00[CHB][hapmap]
rs11900550	1.00[CHB][hapmap]
rs12472020	0.83[EUR][1000 genomes]
rs12477360	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs13389060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13395371	0.84[ASN][1000 genomes]
rs16826952	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16827171	1.00[CHB][hapmap]
rs16827179	1.00[CHB][hapmap]
rs1863674	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1863677	0.84[ASN][1000 genomes]
rs2081713	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2114588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2114590	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2162481	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2396741	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs34839676	0.84[ASN][1000 genomes]
rs3769841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769842	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769846	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs3813464	0.84[ASN][1000 genomes]
rs3820975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3829782	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4343458	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs4972943	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs4972945	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs4972948	1.00[CHB][hapmap]
rs4972951	1.00[CHB][hapmap]
rs4973302	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4973304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4973305	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs4973306	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4973315	1.00[CHB][hapmap]
rs4973317	1.00[CHB][hapmap]
rs4973318	1.00[CHB][hapmap]
rs57003673	0.85[EUR][1000 genomes]
rs57402789	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59020873	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59805999	0.80[EUR][1000 genomes]
rs61575136	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62191186	0.85[EUR][1000 genomes]
rs62191188	0.85[EUR][1000 genomes]
rs62191189	0.80[EUR][1000 genomes]
rs62191191	0.85[EUR][1000 genomes]
rs62191192	0.85[EUR][1000 genomes]
rs62191193	0.83[EUR][1000 genomes]
rs62191196	0.85[EUR][1000 genomes]
rs62191197	0.85[EUR][1000 genomes]
rs62191199	0.85[EUR][1000 genomes]
rs62191200	0.85[EUR][1000 genomes]
rs62191201	0.85[EUR][1000 genomes]
rs62191202	0.85[EUR][1000 genomes]
rs62192161	0.80[EUR][1000 genomes]
rs62193107	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62193138	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62193139	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62193140	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62193141	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62193142	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62193143	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62193147	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6756713	1.00[CHB][hapmap]
rs7576496	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7591582	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9989792	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9989808	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231059000-231082800	Weak transcription	Stomach Mucosa	stomach
2	chr2:231062600-231082400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:231062600-231084200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:231063000-231084000	Weak transcription	Hela-S3	cervix
5	chr2:231063200-231084000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:231064800-231084000	Weak transcription	Fetal Heart	heart
7	chr2:231066200-231083200	Weak transcription	HUVEC	blood vessel
8	chr2:231066200-231084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:231067600-231084200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:231068200-231084400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:231068400-231084000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:231071800-231084200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:231073600-231084000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:231074200-231084000	Weak transcription	Fetal Kidney	kidney
15	chr2:231076000-231084200	Weak transcription	Brain Angular Gyrus	brain
16	chr2:231076800-231084000	Weak transcription	NHDF-Ad	bronchial
17	chr2:231077400-231084000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:231077400-231084000	Weak transcription	NH-A	brain
19	chr2:231077400-231084000	Weak transcription	Osteobl	bone
20	chr2:231077400-231084200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:231077600-231084000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:231077800-231082800	Weak transcription	HepG2	liver
23	chr2:231077800-231084000	Weak transcription	NHLF	lung
24	chr2:231078000-231082600	Weak transcription	Colonic Mucosa	Colon
25	chr2:231078000-231082600	Weak transcription	Psoas Muscle	Psoas
26	chr2:231078000-231084200	Weak transcription	Pancreas	Pancrea
27	chr2:231078800-231082600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:231079000-231082400	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:231079000-231084000	Weak transcription	Brain Anterior Caudate	brain
30	chr2:231079200-231082400	Weak transcription	Brain Substantia Nigra	brain
31	chr2:231079200-231083200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:231079200-231083800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:231079200-231084200	Weak transcription	Esophagus	oesophagus
34	chr2:231079600-231082400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:231079800-231083200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:231079800-231084200	Weak transcription	Gastric	stomach
37	chr2:231080200-231082400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr2:231080200-231082600	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr2:231080600-231082600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
40	chr2:231080600-231082600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:231080600-231082800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:231080600-231083000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:231080600-231083600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:231080800-231084200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:231080800-231084200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:231081000-231083000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr2:231081000-231083800	Enhancers	HMEC	breast
48	chr2:231081000-231084200	Weak transcription	Fetal Intestine Large	intestine
49	chr2:231081200-231082400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:231081200-231082600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links