Variant report

Variant	rs3217901
Chromosome Location	chr12:4405389-4405390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs3217874	0.81[JPT][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv832317	chr12:4315298-4435615	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv541361	chr12:4362258-4413849	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1042204	chr12:4395088-4408802	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1054861	chr12:4395342-4406281	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1037515	chr12:4395342-4408673	Enhancers Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1035984	chr12:4395342-4408802	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1035841	chr12:4395736-4408802	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1053259	chr12:4396376-4408802	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv468984	chr12:4399087-4411804	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
11	nsv557121	chr12:4399087-4411804	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Colorectal cancer	23266556	GWAS catalog

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4386600-4406800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:4387200-4415200	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr12:4387800-4415200	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:4388200-4411200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:4388200-4415200	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr12:4388200-4415200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:4390000-4405800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
8	chr12:4394000-4410200	Weak transcription	Thymus	Thymus
9	chr12:4397200-4415800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:4397400-4415000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:4397400-4416000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:4397600-4409800	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr12:4397600-4415000	Strong transcription	NHEK	skin
14	chr12:4397600-4415400	Strong transcription	HMEC	breast
15	chr12:4398200-4411600	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:4398200-4412800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:4398800-4411000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr12:4398800-4417400	Strong transcription	GM12878-XiMat	blood
19	chr12:4399000-4411400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:4399000-4416800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:4399000-4417200	Weak transcription	Gastric	stomach
22	chr12:4399400-4411200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:4399400-4416200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr12:4399600-4420000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:4399800-4419400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:4400000-4405400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:4400000-4410200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:4400000-4413200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:4400000-4415200	Strong transcription	Primary hematopoietic stem cells	blood
30	chr12:4400000-4418800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:4400800-4406800	Weak transcription	Pancreas	Pancrea
32	chr12:4401400-4406200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:4401600-4411200	Weak transcription	HSMMtube	muscle
34	chr12:4402000-4415600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr12:4402800-4406800	Weak transcription	HSMM	muscle
36	chr12:4402800-4411200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr12:4403000-4406200	Strong transcription	Lung	lung
38	chr12:4403000-4412600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:4403000-4416000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:4403000-4416800	Weak transcription	Fetal Kidney	kidney
41	chr12:4403200-4405600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
42	chr12:4403200-4413800	Strong transcription	Fetal Lung	lung
43	chr12:4403200-4415200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:4403200-4416400	Strong transcription	Primary B cells from cord blood	blood
45	chr12:4403200-4419000	Strong transcription	Primary T cells from cord blood	blood
46	chr12:4403200-4419200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:4403400-4405600	Genic enhancers	Stomach Smooth Muscle	stomach
48	chr12:4403400-4406400	Strong transcription	Colonic Mucosa	Colon
49	chr12:4403400-4407200	Strong transcription	Spleen	Spleen
50	chr12:4403400-4409200	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links