Variant report

Variant	rs12641297
Chromosome Location	chr4:151834657-151834658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151832868..151835520-chr4:151835576..151838225,3	K562	blood:
2	chr4:151834153..151836017-chr4:151935343..151937971,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198589	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10006912	0.80[EUR][1000 genomes]
rs10031124	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10520078	0.80[JPT][hapmap];0.94[TSI][hapmap]
rs10857252	0.84[EUR][1000 genomes]
rs10857253	0.89[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs11099780	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11099781	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1148645	0.97[ASN][1000 genomes]
rs1148652	0.94[ASN][1000 genomes]
rs11733964	0.94[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs11934912	0.80[EUR][1000 genomes]
rs1201198	0.96[ASN][1000 genomes]
rs1201208	0.85[GIH][hapmap]
rs1201210	0.82[GIH][hapmap]
rs1201214	0.96[ASN][1000 genomes]
rs13101417	0.94[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs13112801	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13126862	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13141515	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs13145482	0.93[YRI][hapmap]
rs13145829	0.94[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs1365380	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2098927	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407548	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407549	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2897659	0.94[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs4696640	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4696649	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4696658	0.94[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs6848445	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6854299	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7441414	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7665654	0.80[EUR][1000 genomes]
rs7677374	0.85[GIH][hapmap]
rs7690977	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7691797	0.80[EUR][1000 genomes]
rs7693278	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs891689	0.85[GIH][hapmap]
rs9997773	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1024820	chr4:151364078-151943561	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1018404	chr4:151664438-152067409	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv1017850	chr4:151664438-152071876	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' 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	35 gene(s)	inside rSNPs	diseases
8	esv2763837	chr4:151664438-152071888	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv870257	chr4:151665349-152072867	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv1015387	chr4:151673751-152071876	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv526976	chr4:151675819-152055073	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	nsv1025077	chr4:151682266-152035733	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	nsv537303	chr4:151682266-152035733	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv949066	chr4:151693149-152069566	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
15	nsv949002	chr4:151693149-152095109	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
16	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
17	nsv1031720	chr4:151708502-152071876	Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
18	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
19	nsv1031516	chr4:151718614-152065644	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
20	nsv537304	chr4:151718614-152065644	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
21	nsv1022884	chr4:151718814-152065505	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
22	nsv537305	chr4:151718814-152065505	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
23	nsv880576	chr4:151751369-151936149	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
24	nsv595689	chr4:151788955-152015704	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
25	nsv595690	chr4:151788955-152109552	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS 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	35 gene(s)	inside rSNPs	diseases
26	nsv1032391	chr4:151804133-151850074	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
27	nsv1029464	chr4:151817148-151868929	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
28	nsv881254	chr4:151829824-151936149	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151774000-151838400	Weak transcription	HepG2	liver
2	chr4:151796000-151845000	Weak transcription	Fetal Heart	heart
3	chr4:151796000-151846000	Weak transcription	Aorta	Aorta
4	chr4:151796000-151847200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:151796200-151849600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:151796200-151872000	Weak transcription	Psoas Muscle	Psoas
7	chr4:151796400-151855000	Weak transcription	Gastric	stomach
8	chr4:151796400-151886600	Weak transcription	Pancreas	Pancrea
9	chr4:151796800-151851000	Weak transcription	Lung	lung
10	chr4:151799600-151839600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:151806600-151839800	Weak transcription	HSMMtube	muscle
12	chr4:151806800-151851600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:151806800-151860400	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:151808200-151837000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:151810200-151843600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:151811800-151852800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:151812000-151857800	Weak transcription	NH-A	brain
18	chr4:151813600-151847000	Weak transcription	Brain Angular Gyrus	brain
19	chr4:151813800-151837200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:151814600-151834800	Weak transcription	Placenta	Placenta
21	chr4:151820800-151838600	Weak transcription	NHDF-Ad	bronchial
22	chr4:151821400-151850800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:151821800-151839800	Weak transcription	Hela-S3	cervix
24	chr4:151823000-151841600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:151824200-151836600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr4:151824800-151843800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:151824800-151845400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:151824800-151851200	Weak transcription	Esophagus	oesophagus
29	chr4:151825200-151834800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:151825200-151850800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:151828000-151843800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:151828200-151835000	Weak transcription	Adipose Nuclei	Adipose
33	chr4:151828200-151847000	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:151828600-151850600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:151828800-151850400	Weak transcription	Colonic Mucosa	Colon
36	chr4:151829200-151837000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:151829200-151837800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:151829200-151843000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:151829400-151840400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:151829600-151839200	Strong transcription	Liver	Liver
41	chr4:151830400-151835400	ZNF genes & repeats	GM12878-XiMat	blood
42	chr4:151830400-151838000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:151830400-151838000	Strong transcription	Fetal Thymus	thymus
44	chr4:151830600-151837200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr4:151830800-151836400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:151831000-151836400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:151831200-151835000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:151831200-151836000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:151831600-151838000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:151831800-151837800	Strong transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links