Variant report

Variant	rs11762273
Chromosome Location	chr7:98977187-98977188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:98976910..98979073-chr7:98989172..98991412,2	MCF-7	breast:
2	chr7:98975447..98980936-chr7:99003746..99008536,8	MCF-7	breast:
3	chr7:98927030..98929384-chr7:98976181..98977844,2	MCF-7	breast:
4	chr7:98975439..98979350-chr7:99003635..99008025,5	K562	blood:
5	chr7:98976344..98978332-chr7:98985918..98989033,3	MCF-7	breast:
6	chr7:98965082..98967314-chr7:98975254..98977961,2	K562	blood:
7	chr7:98976192..98977767-chr7:99011584..99014530,2	MCF-7	breast:
8	chr7:98975550..98978554-chr7:98995134..98998882,4	K562	blood:
9	chr7:98977091..98978617-chr7:99034122..99036702,2	MCF-7	breast:
10	chr17:66637981..66640873-chr7:98975754..98977781,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000239133	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000130429	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10155966	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10236149	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10238965	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs10243678	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10249167	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10255399	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10258757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10267346	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10270459	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10270917	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10271049	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap]
rs10272998	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10274407	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10277149	0.82[EUR][1000 genomes]
rs10279308	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1043466	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap]
rs10953286	0.91[GIH][hapmap];1.00[YRI][hapmap]
rs10953287	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11771702	0.83[CEU][hapmap]
rs11973460	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11976018	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap]
rs11978089	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs12112936	0.83[CEU][hapmap]
rs12113440	0.83[CEU][hapmap]
rs13240600	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs17161695	0.83[CEU][hapmap]
rs17161698	0.91[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1980307	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs1985453	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs2003499	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2057905	0.88[ASN][1000 genomes]
rs2057906	0.89[ASN][1000 genomes]
rs2072181	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2107922	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2240384	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap]
rs2269985	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2272168	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs2280600	0.83[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs2280601	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap]
rs2286162	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2301889	0.82[CHD][hapmap]
rs2404322	0.90[ASN][1000 genomes]
rs2404323	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28495024	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28820905	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3137	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs3764815	0.90[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3779354	0.89[JPT][hapmap]
rs3801288	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3843540	0.83[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs4729532	0.92[ASW][hapmap];0.91[CEU][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs59986060	0.81[ASN][1000 genomes]
rs6943920	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6953476	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6955490	0.92[ASW][hapmap];0.91[CEU][hapmap];0.83[MKK][hapmap];0.86[EUR][1000 genomes]
rs6962772	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap]
rs6972337	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6975099	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs733991	0.83[CEU][hapmap]
rs7794705	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs883403	0.92[CEU][hapmap]
rs917154	0.91[ASW][hapmap];0.91[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap]
rs9641253	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9768020	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11762273	ZKSCAN1	cis	parietal	SCAN
rs11762273	ARPC1B	cis	Thyroid	GTEx
rs11762273	OR2AE1	cis	parietal	SCAN
rs11762273	GATS	cis	parietal	SCAN
rs11762273	CPSF4	cis	parietal	SCAN
rs11762273	ACTL6B	cis	cerebellum	SCAN
rs11762273	PILRA	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98971000-98990400	Weak transcription	Fetal Kidney	kidney
2	chr7:98973200-98978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:98973400-98977200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:98973400-98977200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:98973400-98977200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:98973400-98977200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:98973400-98977600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:98973400-98977600	Weak transcription	Brain Substantia Nigra	brain
9	chr7:98973400-98977600	Weak transcription	Fetal Heart	heart
10	chr7:98973400-98977600	Weak transcription	Small Intestine	intestine
11	chr7:98973400-98978400	Weak transcription	Psoas Muscle	Psoas
12	chr7:98973400-98978600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:98973400-98978800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:98973400-98979000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr7:98973400-98979200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:98973400-98984000	Weak transcription	Aorta	Aorta
17	chr7:98973400-98984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:98973400-98984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:98973400-98984200	Weak transcription	Ovary	ovary
20	chr7:98973400-98984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:98973400-98987400	Weak transcription	Brain Germinal Matrix	brain
22	chr7:98973400-98987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:98973400-98989800	Weak transcription	Brain Angular Gyrus	brain
24	chr7:98973800-98977200	Weak transcription	Left Ventricle	heart
25	chr7:98974000-98977600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr7:98974200-98978200	Weak transcription	Pancreas	Pancrea
27	chr7:98974600-98977200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:98974800-98979800	Strong transcription	Fetal Intestine Small	intestine
29	chr7:98975000-98978400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr7:98975800-98977200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:98976000-98977400	Weak transcription	Lung	lung
32	chr7:98976000-98977600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:98976400-98977600	Weak transcription	Fetal Intestine Large	intestine
34	chr7:98976600-98977200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:98976600-98977200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:98976600-98977200	Enhancers	Fetal Thymus	thymus
37	chr7:98976600-98977200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr7:98976600-98977200	Enhancers	NHDF-Ad	bronchial
39	chr7:98976600-98977200	Enhancers	NHLF	lung
40	chr7:98976600-98977200	Enhancers	Osteobl	bone
41	chr7:98976600-98977600	Genic enhancers	Dnd41	blood
42	chr7:98976600-98978200	Flanking Active TSS	Hela-S3	cervix
43	chr7:98976600-98978200	Enhancers	HepG2	liver
44	chr7:98976600-98978400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:98976600-98978600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr7:98976600-98978600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr7:98976600-98978600	Enhancers	NH-A	brain
48	chr7:98976600-98978800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:98976600-98978800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr7:98976600-98978800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links