Variant report

Variant	rs2671267
Chromosome Location	chr1:226025690-226025691
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226015474..226017647-chr1:226024996..226027298,2	MCF-7	breast:
2	chr1:226022223..226024431-chr1:226025111..226027659,2	MCF-7	breast:
3	chr1:226025653..226027789-chr1:226114675..226116510,2	K562	blood:

Variant related genes	Relation type
ENSG00000143819	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1051741	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2234922	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs2292558	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2671264	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2671266	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2740174	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56108141	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv947519	chr1:225998770-226034631	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv945328	chr1:226015604-226031170	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2671267	MIA3	cis	cerebellum	SCAN
rs2671267	LEFTY2	cis	cerebellum	SCAN
rs2671267	ZNF678	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226013400-226031800	Weak transcription	Fetal Kidney	kidney
2	chr1:226013600-226052600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:226013800-226032000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:226013800-226037200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:226014000-226032800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:226014600-226035600	Weak transcription	Small Intestine	intestine
7	chr1:226014800-226047800	Weak transcription	Psoas Muscle	Psoas
8	chr1:226015400-226026400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:226015400-226032400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:226015400-226033200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:226015600-226033600	Weak transcription	K562	blood
12	chr1:226016000-226051000	Weak transcription	NH-A	brain
13	chr1:226016400-226033400	Strong transcription	Fetal Intestine Small	intestine
14	chr1:226016800-226033600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr1:226017400-226049800	Weak transcription	HUVEC	blood vessel
16	chr1:226018600-226025800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:226019800-226026200	Weak transcription	Brain Germinal Matrix	brain
18	chr1:226020000-226025800	Weak transcription	Thymus	Thymus
19	chr1:226020000-226026000	Weak transcription	Colonic Mucosa	Colon
20	chr1:226020200-226027000	Weak transcription	HSMMtube	muscle
21	chr1:226020400-226032000	Weak transcription	Aorta	Aorta
22	chr1:226020400-226033400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:226020600-226026200	Weak transcription	Brain Anterior Caudate	brain
24	chr1:226020600-226027600	Weak transcription	Primary T cells from cord blood	blood
25	chr1:226020600-226042000	Weak transcription	Hela-S3	cervix
26	chr1:226020600-226042400	Weak transcription	HSMM	muscle
27	chr1:226020800-226025800	Weak transcription	Fetal Brain Female	brain
28	chr1:226020800-226026000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:226020800-226033400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:226020800-226033800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:226021000-226026000	Weak transcription	Fetal Intestine Large	intestine
32	chr1:226021000-226033400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:226021200-226026000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:226021200-226026400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:226021400-226026400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:226022200-226033200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:226022200-226033200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:226022400-226028000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:226022600-226028200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:226022800-226025800	Weak transcription	Esophagus	oesophagus
41	chr1:226022800-226025800	Weak transcription	Osteobl	bone
42	chr1:226022800-226026000	Weak transcription	Gastric	stomach
43	chr1:226022800-226026000	Weak transcription	NHLF	lung
44	chr1:226022800-226026200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:226022800-226026400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:226022800-226026400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:226022800-226026600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:226022800-226029800	Weak transcription	Fetal Thymus	thymus
49	chr1:226022800-226030000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:226022800-226033800	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links