Variant report

Variant	rs12947238
Chromosome Location	chr17:37555226-37555227
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	chr17:37553983..37556273-chr17:37556304..37558931,2	K562	blood:
2	chr17:37553969..37556475-chr17:37564742..37566292,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108306	Chromatin interaction
ENSG00000266469	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12940109	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12940881	1.00[AMR][1000 genomes]
rs12940956	1.00[AMR][1000 genomes]
rs12945363	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12953178	1.00[AMR][1000 genomes]
rs34362498	0.87[AFR][1000 genomes]
rs34821956	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34904106	1.00[AMR][1000 genomes]
rs34910003	1.00[AMR][1000 genomes]
rs34983824	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35194764	1.00[AMR][1000 genomes]
rs35269184	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35366897	1.00[AMR][1000 genomes]
rs35499078	1.00[AMR][1000 genomes]
rs35656573	1.00[AMR][1000 genomes]
rs35829705	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35853230	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35896550	1.00[AMR][1000 genomes]
rs57938769	1.00[AMR][1000 genomes]
rs59775294	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6503512	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71369747	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs71369760	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs71369763	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71369765	1.00[AMR][1000 genomes]
rs71369767	1.00[AMR][1000 genomes]
rs71577045	0.83[AMR][1000 genomes]
rs7212530	1.00[AMR][1000 genomes]
rs7212780	1.00[AMR][1000 genomes]
rs7218668	1.00[AMR][1000 genomes]
rs7226222	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8064372	1.00[AMR][1000 genomes]
rs8069194	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8073144	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8074199	1.00[AMR][1000 genomes]
rs8076843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8077259	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8077629	0.85[AFR][1000 genomes]
rs8077822	1.00[AMR][1000 genomes]
rs8079346	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8080830	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8081561	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9747574	1.00[AMR][1000 genomes]
rs9747666	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1060126	chr17:37333956-37659189	Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv1057655	chr17:37333956-37732451	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
5	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
6	nsv908204	chr17:37349655-37682657	Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv1057057	chr17:37395082-37627025	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1055612	chr17:37409865-37563236	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1061951	chr17:37442228-37770903	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
10	nsv543341	chr17:37442228-37770903	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
11	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
12	nsv532712	chr17:37521822-37768345	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37498800-37556400	Weak transcription	Thymus	Thymus
2	chr17:37514800-37556200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:37515400-37555600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr17:37517600-37556600	Weak transcription	Fetal Muscle Leg	muscle
5	chr17:37522600-37555400	Weak transcription	Fetal Lung	lung
6	chr17:37522600-37556200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr17:37522800-37555400	Weak transcription	Adipose Nuclei	Adipose
8	chr17:37522800-37556400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:37523400-37556200	Weak transcription	Ovary	ovary
10	chr17:37523600-37555800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr17:37530200-37555600	Weak transcription	Primary T cells from cord blood	blood
12	chr17:37533200-37556200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr17:37533200-37556600	Weak transcription	Pancreas	Pancrea
14	chr17:37534200-37556200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr17:37534400-37555600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:37534400-37555800	Weak transcription	Hela-S3	cervix
17	chr17:37534400-37556200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:37536800-37556000	Weak transcription	Brain Anterior Caudate	brain
19	chr17:37537000-37555600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr17:37537000-37556200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:37537000-37556200	Weak transcription	Brain Hippocampus Middle	brain
22	chr17:37538800-37555600	Weak transcription	Primary B cells from cord blood	blood
23	chr17:37539200-37556800	Weak transcription	Gastric	stomach
24	chr17:37541400-37555600	Weak transcription	Brain Angular Gyrus	brain
25	chr17:37541600-37556800	Weak transcription	Lung	lung
26	chr17:37541600-37557000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:37542800-37555800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:37543200-37555600	Weak transcription	Fetal Brain Female	brain
29	chr17:37543400-37556600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:37543600-37555400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr17:37543600-37556000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr17:37544400-37556200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr17:37544600-37556000	Weak transcription	Fetal Stomach	stomach
34	chr17:37544600-37556400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr17:37544600-37556400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr17:37544600-37556600	Weak transcription	Fetal Thymus	thymus
37	chr17:37544800-37555600	Weak transcription	Liver	Liver
38	chr17:37544800-37555800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr17:37544800-37556200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr17:37544800-37556400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr17:37544800-37556600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr17:37544800-37556600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr17:37545000-37556600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr17:37545200-37556600	Weak transcription	Placenta	Placenta
45	chr17:37545800-37555600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:37548600-37556600	Weak transcription	Left Ventricle	heart
47	chr17:37550400-37555800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr17:37550400-37556000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr17:37550400-37556400	Weak transcription	HSMM	muscle
50	chr17:37552400-37556400	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links