Variant report

Variant	rs6691216
Chromosome Location	chr1:197659263-197659264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr1:197659213-197659583	K562	blood:	n/a	chr1:197659378-197659389
2	POLR2A	chr1:197659226-197659465	ProgFib	skin:	n/a	n/a
3	ATF1	chr1:197659216-197659501	K562	blood:	n/a	n/a
4	FOSL1	chr1:197659150-197659608	K562	blood:	n/a	n/a
5	ATF3	chr1:197659190-197659476	K562	blood:	n/a	n/a
6	USF1	chr1:197659224-197659578	K562	blood:	n/a	n/a
7	CBX3	chr1:197659156-197659567	K562	blood:	n/a	n/a
8	USF1	chr1:197659171-197659560	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197652165..197657690-chr1:197657725..197663370,6	K562	blood:

Variant related genes	Relation type
ENSG00000207139	TF binding region
ENSG00000207139	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10754228	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10801620	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10922252	0.81[ASN][1000 genomes]
rs10922259	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10922260	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10922266	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042609	0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs12066841	0.92[ASN][1000 genomes]
rs12081207	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs1998711	0.92[ASN][1000 genomes]
rs2111930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2111934	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4026508	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4026514	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4274099	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4282851	0.95[ASN][1000 genomes]
rs4611052	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4915561	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.83[ASN][1000 genomes]
rs55995691	0.90[ASN][1000 genomes]
rs6428416	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6667560	0.82[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs6667685	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6675292	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs6688289	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516153	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7516334	0.89[ASN][1000 genomes]
rs7516481	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.89[ASN][1000 genomes]
rs7523627	0.91[ASN][1000 genomes]
rs7533766	0.94[ASN][1000 genomes]
rs7548454	0.95[ASN][1000 genomes]
rs9633354	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv437263	chr1:197599030-197722240	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv873077	chr1:197615391-197698103	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv946566	chr1:197659060-197661728	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6691216	LHX2	trans	parietal	SCAN
rs6691216	DENND1B	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197645200-197661000	Weak transcription	Esophagus	oesophagus
2	chr1:197653000-197665200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:197653000-197665400	Weak transcription	Osteobl	bone
4	chr1:197653200-197659400	Weak transcription	Left Ventricle	heart
5	chr1:197653200-197660600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:197653400-197662000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:197653600-197660600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:197653600-197660800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:197654600-197662200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:197656000-197662000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:197656200-197659600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:197656200-197663600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:197656400-197660400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:197657000-197677000	Weak transcription	Ovary	ovary
15	chr1:197657800-197663400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:197658000-197659600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr1:197658000-197661000	Weak transcription	Liver	Liver
18	chr1:197658000-197661000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:197658000-197665200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:197658200-197659400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:197658200-197659400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:197658200-197659400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr1:197658200-197659600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:197658200-197660400	Weak transcription	Fetal Lung	lung
25	chr1:197658200-197660600	Weak transcription	Colonic Mucosa	Colon
26	chr1:197658200-197662000	Weak transcription	Thymus	Thymus
27	chr1:197658200-197662800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:197658200-197668200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:197658400-197659400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:197658400-197659600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr1:197658400-197659800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
32	chr1:197658400-197665000	Weak transcription	NHEK	skin
33	chr1:197658600-197659600	ZNF genes & repeats	Primary T cells from cord blood	blood
34	chr1:197658600-197662000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:197658800-197659600	Strong transcription	Primary B cells from cord blood	blood
36	chr1:197658800-197659600	Genic enhancers	K562	blood
37	chr1:197658800-197659800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:197658800-197659800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:197659000-197659400	Strong transcription	Fetal Thymus	thymus
40	chr1:197659000-197659600	Strong transcription	Fetal Intestine Large	intestine
41	chr1:197659000-197659600	Strong transcription	Gastric	stomach
42	chr1:197659000-197659600	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:197659200-197659800	Strong transcription	Primary hematopoietic stem cells	blood
44	chr1:197659200-197659800	Strong transcription	Dnd41	blood

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