Variant report

Variant	rs2237152
Chromosome Location	chr6:15404250-15404251
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15397507..15402114-chr6:15402418..15406858,9	K562	blood:
2	chr6:15402174..15407413-chr6:15410357..15414538,6	K562	blood:
3	chr6:15401226..15405320-chr6:15407295..15410337,3	K562	blood:
4	chr6:15395497..15398020-chr6:15401720..15405105,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2072819	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2072820	0.95[CHB][hapmap]
rs2237149	0.88[EUR][1000 genomes]
rs2237150	0.88[CEU][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs2237153	0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237156	0.84[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs2237157	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237159	0.95[CHB][hapmap]
rs2237160	0.95[CHB][hapmap]
rs2299048	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs2299053	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs2299054	0.84[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2299059	0.91[CHD][hapmap]
rs6905698	0.95[CHB][hapmap]
rs6924733	0.95[CHB][hapmap]
rs9349978	0.88[EUR][1000 genomes]
rs9358059	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9358060	0.88[EUR][1000 genomes]
rs9370813	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs9383051	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9383054	0.84[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs9464785	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9464786	0.90[CHB][hapmap]
rs9464787	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9476820	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1019927	chr6:15351240-15419257	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv538145	chr6:15351240-15419257	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2237152	AF454553	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15396200-15410200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr6:15397400-15405600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:15397600-15405800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:15398000-15406000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr6:15398400-15405600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:15398600-15405800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr6:15398600-15406600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr6:15399000-15410600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:15400200-15406000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:15400200-15406200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:15400400-15412800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:15400600-15406600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr6:15400800-15411200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:15401200-15404400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr6:15401200-15404400	Weak transcription	Osteobl	bone
16	chr6:15401200-15404800	Enhancers	Fetal Muscle Leg	muscle
17	chr6:15401200-15405200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:15401200-15405200	Enhancers	Fetal Intestine Large	intestine
19	chr6:15401200-15405600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:15401200-15405800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:15401200-15405800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr6:15401200-15405800	Enhancers	Fetal Intestine Small	intestine
23	chr6:15401200-15406000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr6:15401200-15406000	Enhancers	Fetal Lung	lung
25	chr6:15401200-15406200	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:15401200-15406400	Weak transcription	Gastric	stomach
27	chr6:15401200-15407600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:15401200-15414000	Weak transcription	Aorta	Aorta
29	chr6:15401200-15417200	Weak transcription	Lung	lung
30	chr6:15401200-15426200	Weak transcription	Pancreas	Pancrea
31	chr6:15401400-15404400	Weak transcription	Adipose Nuclei	Adipose
32	chr6:15401400-15405000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr6:15401400-15405400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr6:15401400-15406200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr6:15401400-15406800	Enhancers	K562	blood
36	chr6:15401400-15411600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr6:15401600-15406000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:15401600-15415800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:15401800-15405400	Enhancers	Brain Substantia Nigra	brain
40	chr6:15402200-15405200	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr6:15402200-15406200	Enhancers	Psoas Muscle	Psoas
42	chr6:15402400-15405000	Enhancers	Thymus	Thymus
43	chr6:15402400-15405200	Enhancers	Small Intestine	intestine
44	chr6:15402400-15406600	Enhancers	Fetal Thymus	thymus
45	chr6:15402400-15406600	Enhancers	Left Ventricle	heart
46	chr6:15402400-15407000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:15402600-15404400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:15402600-15404600	Enhancers	Right Ventricle	heart
49	chr6:15402600-15413600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:15402800-15404600	Weak transcription	Colon Smooth Muscle	Colon

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