Variant report

Variant	rs4289171
Chromosome Location	chr2:209000144-209000145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:208995156..208996689-chr2:208999145..209001053,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11678616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11679743	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12464752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392731	0.88[MEX][hapmap]
rs2242071	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs4263096	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4276012	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4338947	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449112	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583446	0.89[JPT][hapmap]
rs6435416	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710715	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711499	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751246	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578859	0.88[MEX][hapmap]
rs796287	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv875747	chr2:208990345-209042963	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv875748	chr2:208994399-209033557	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4289171	C2orf67	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208993400-209002200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:208994600-209002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:208998400-209000400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:208998800-209002000	Enhancers	Fetal Intestine Small	intestine
5	chr2:208998800-209002400	Enhancers	Fetal Intestine Large	intestine
6	chr2:208999000-209000800	Enhancers	Primary hematopoietic stem cells	blood
7	chr2:208999000-209000800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:208999200-209000400	Enhancers	Duodenum Mucosa	Duodenum
9	chr2:208999200-209000600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr2:208999200-209000600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:208999200-209002200	Enhancers	HepG2	liver
12	chr2:208999400-209000200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:208999400-209000400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr2:208999400-209000400	Enhancers	Thymus	Thymus
15	chr2:208999400-209000600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:208999400-209000800	Enhancers	Fetal Thymus	thymus
17	chr2:208999400-209000800	Enhancers	Dnd41	blood
18	chr2:208999600-209000200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:208999600-209000200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr2:208999600-209000400	Enhancers	HMEC	breast
21	chr2:208999600-209000600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:208999600-209000800	Enhancers	Primary T cells from cord blood	blood
23	chr2:208999600-209002000	Enhancers	Ovary	ovary
24	chr2:208999600-209002000	Enhancers	Stomach Mucosa	stomach
25	chr2:208999800-209000200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:208999800-209000200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr2:208999800-209000200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr2:208999800-209000400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:208999800-209000400	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr2:208999800-209000400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:208999800-209000400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:208999800-209000600	Enhancers	Placenta	Placenta
33	chr2:208999800-209000600	Enhancers	Pancreas	Pancrea
34	chr2:208999800-209000800	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr2:209000000-209000400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:209000000-209000800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:209000000-209000800	Enhancers	Small Intestine	intestine

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