Variant report

Variant	rs7761966
Chromosome Location	chr6:27445703-27445704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr6:27445346-27445941	HL-60	blood:	n/a	n/a
2	SREBP2	chr6:27445144-27448922	GM12878	blood:	n/a	n/a
3	TEAD4	chr6:27445622-27447858	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27445180..27448158-chr6:27859004..27861721,2	K562	blood:
2	chr6:27440158..27442625-chr6:27445156..27448200,3	MCF-7	breast:
3	chr6:27444748..27447549-chr6:27506733..27508413,2	K562	blood:
4	chr6:27436780..27444180-chr6:27444326..27451609,21	K562	blood:
5	chr6:27445237..27448966-chr6:27511451..27515137,4	K562	blood:
6	chr6:27444529..27447552-chr6:27720507..27722383,3	K562	blood:
7	chr6:27439314..27444184-chr6:27444600..27448871,6	MCF-7	breast:
8	chr6:27278606..27280267-chr6:27443995..27446330,2	K562	blood:
9	chr6:27445186..27449983-chr6:27468978..27472948,6	K562	blood:
10	chr6:27443187..27445951-chr6:27477606..27480333,4	K562	blood:
11	chr6:27299766..27302375-chr6:27444830..27446395,2	K562	blood:
12	chr6:27445490..27447467-chr6:27449850..27451759,2	K562	blood:
13	chr6:27445490..27447223-chr6:27448748..27451759,4	K562	blood:
14	chr6:27444179..27448029-chr6:27462358..27468433,6	K562	blood:
15	chr6:27445045..27447586-chr6:27780627..27782678,2	MCF-7	breast:
16	chr6:27434893..27436769-chr6:27444407..27446972,3	K562	blood:

No data

Variant related genes	Relation type
ZNF184	TF binding region
ENSG00000197153	Chromatin interaction
ENSG00000158553	Chromatin interaction
ENSG00000096654	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000182611	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1011665	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs10946915	0.88[AMR][1000 genomes]
rs10946935	0.86[LWK][hapmap];0.88[YRI][hapmap]
rs10946940	0.86[LWK][hapmap];0.81[YRI][hapmap]
rs12526495	0.86[AMR][1000 genomes]
rs12529458	0.86[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs12529756	0.91[ASN][1000 genomes]
rs12663650	1.00[YRI][hapmap]
rs12664996	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs13220817	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs1883403	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs2064093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205829	0.91[ASN][1000 genomes]
rs2235232	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2393962	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2393963	0.91[ASN][1000 genomes]
rs2393964	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711152	0.89[AMR][1000 genomes]
rs4711154	1.00[ASN][1000 genomes]
rs4711155	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713098	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4713099	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6456799	0.81[YRI][hapmap]
rs6913166	0.98[GIH][hapmap];0.84[MEX][hapmap]
rs6914864	0.87[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs6915266	0.88[LWK][hapmap];0.88[YRI][hapmap]
rs9393813	0.95[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv883508	chr6:27434220-27455625	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7761966	ZNF391	cis	parietal	SCAN
rs7761966	ZNF391	cis	lung	GTEx
rs7761966	ZNF204P	cis	parietal	SCAN
rs7761966	BTN3A3	cis	cerebellum	SCAN
rs7761966	ZNF391	cis	cerebellum	SCAN
rs7761966	HIST1H2AJ	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27441400-27446000	Weak transcription	Gastric	stomach
2	chr6:27441400-27446000	Weak transcription	Lung	lung
3	chr6:27441400-27446400	Weak transcription	Small Intestine	intestine
4	chr6:27441400-27446800	Weak transcription	Spleen	Spleen
5	chr6:27441600-27445800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr6:27441600-27445800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:27441600-27446000	Weak transcription	Left Ventricle	heart
8	chr6:27441600-27446000	Weak transcription	HSMMtube	muscle
9	chr6:27441800-27445800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:27441800-27445800	Weak transcription	Colonic Mucosa	Colon
11	chr6:27441800-27445800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:27441800-27446000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:27441800-27446000	Weak transcription	Pancreas	Pancrea
14	chr6:27441800-27446000	Weak transcription	HSMM	muscle
15	chr6:27442000-27445800	Weak transcription	Fetal Intestine Large	intestine
16	chr6:27442000-27445800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:27442000-27445800	Weak transcription	Placenta	Placenta
18	chr6:27442000-27445800	Weak transcription	Fetal Thymus	thymus
19	chr6:27442200-27445800	Weak transcription	Right Atrium	heart
20	chr6:27442200-27445800	Weak transcription	NH-A	brain
21	chr6:27442200-27446000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:27444800-27445800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:27444800-27445800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr6:27445000-27445800	Enhancers	Primary B cells from cord blood	blood
25	chr6:27445000-27445800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr6:27445000-27445800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:27445000-27445800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:27445000-27445800	Enhancers	Aorta	Aorta
29	chr6:27445000-27445800	Enhancers	Psoas Muscle	Psoas
30	chr6:27445000-27445800	Enhancers	HepG2	liver
31	chr6:27445000-27446400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr6:27445000-27446400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:27445000-27446400	Flanking Active TSS	K562	blood
34	chr6:27445000-27447800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:27445000-27448000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:27445000-27448000	Active TSS	NHLF	lung
37	chr6:27445200-27445800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr6:27445200-27445800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr6:27445200-27445800	Enhancers	Primary T cells from cord blood	blood
40	chr6:27445200-27445800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr6:27445200-27446000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr6:27445200-27446000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:27445200-27446400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr6:27445200-27446400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:27445200-27448000	Active TSS	H9 Cell Line	embryonic stem cell
46	chr6:27445400-27445800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:27445400-27445800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:27445400-27445800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:27445400-27445800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:27445400-27445800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links