Variant report

Variant	rs11125993
Chromosome Location	chr2:64438890-64438891
allele	C/T
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	NFE2	chr2:64438860-64439015	GM12878	blood:	n/a	n/a
2	USF2	chr2:64438770-64438947	H1-hESC	embryonic stem cell:	n/a	n/a
3	SPI1	chr2:64438332-64439102	HL-60	blood:	n/a	n/a
4	USF2	chr2:64438849-64439006	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:64432532..64434467-chr2:64436977..64439026,2	K562	blood:
2	chr2:64437286..64442036-chr2:64442990..64448045,5	K562	blood:
3	chr2:64438408..64440194-chr2:64451876..64454723,2	K562	blood:

Variant related genes	Relation type
ENSG00000270354	TF binding region
ENSG00000225889	Chromatin interaction
ENSG00000230923	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10496110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs11125992	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11125994	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688386	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13399701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370388	0.82[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1816617	0.87[ASN][1000 genomes]
rs1816618	0.89[ASN][1000 genomes]
rs2555434	0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2555435	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1004574	chr2:64360195-64478171	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
19	nsv1004899	chr2:64369300-64513607	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
20	nsv535769	chr2:64369300-64513607	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
21	nsv1015084	chr2:64369734-64512286	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
22	nsv874237	chr2:64402689-64479060	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64424400-64440000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:64431600-64440000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:64431600-64441000	Weak transcription	Esophagus	oesophagus
4	chr2:64431600-64446800	Weak transcription	Left Ventricle	heart
5	chr2:64431800-64441000	Weak transcription	Right Atrium	heart
6	chr2:64432000-64441600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:64432200-64440000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:64432200-64441000	Weak transcription	Brain Substantia Nigra	brain
9	chr2:64432400-64440000	Weak transcription	Brain Anterior Caudate	brain
10	chr2:64432400-64440800	Weak transcription	Fetal Intestine Small	intestine
11	chr2:64432400-64441200	Weak transcription	Fetal Lung	lung
12	chr2:64432800-64439000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:64432800-64440200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:64432800-64441200	Weak transcription	Fetal Kidney	kidney
15	chr2:64433000-64440400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:64433000-64441000	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:64433200-64439000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:64435000-64439000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:64435400-64439200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:64435800-64439200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:64435800-64439600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr2:64436000-64440000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:64436400-64442400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr2:64437400-64439000	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr2:64437400-64441000	Enhancers	NHEK	skin
26	chr2:64437400-64442200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:64437600-64439000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:64437600-64440200	Enhancers	Fetal Thymus	thymus
29	chr2:64437600-64441000	Enhancers	Primary B cells from cord blood	blood
30	chr2:64437600-64442400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:64437600-64442600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:64437800-64439000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:64437800-64439000	Enhancers	Duodenum Mucosa	Duodenum
34	chr2:64437800-64439000	Enhancers	Gastric	stomach
35	chr2:64437800-64439000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr2:64437800-64439600	Enhancers	GM12878-XiMat	blood
37	chr2:64437800-64442200	Enhancers	Stomach Mucosa	stomach
38	chr2:64438000-64439000	Enhancers	Colon Smooth Muscle	Colon
39	chr2:64438000-64439000	Enhancers	Placenta	Placenta
40	chr2:64438000-64439200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr2:64438000-64439400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr2:64438000-64440000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:64438000-64441000	Enhancers	Primary B cells from peripheral blood	blood
44	chr2:64438000-64441200	Enhancers	Primary T cells from cord blood	blood
45	chr2:64438000-64441200	Enhancers	Primary hematopoietic stem cells	blood
46	chr2:64438200-64439000	Enhancers	Spleen	Spleen
47	chr2:64438200-64439200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr2:64438200-64439200	Enhancers	Colonic Mucosa	Colon
49	chr2:64438200-64448200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:64438400-64440800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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