Variant report

Variant	rs10243678
Chromosome Location	chr7:98991944-98991945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:98988826..98993566-chr7:99002963..99006762,7	MCF-7	breast:
2	chr7:98923537..98926194-chr7:98989828..98992452,2	K562	blood:
3	chr7:98859553..98861919-chr7:98990748..98992511,2	K562	blood:
4	chr7:98970980..98974747-chr7:98986775..98992580,7	MCF-7	breast:
5	chr7:98971244..98973231-chr7:98989224..98993180,5	MCF-7	breast:
6	chr7:98966757..98974253-chr7:98988800..98995304,7	K562	blood:

Variant related genes	Relation type
ENSG00000130429	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000002079	Chromatin interaction
ENSG00000241685	Chromatin interaction
ENSG00000106245	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10155966	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10236149	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10238965	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs10244158	0.80[AMR][1000 genomes]
rs10249167	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10255399	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10258757	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];0.91[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10267346	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10270459	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10270917	0.83[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];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10271049	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10272998	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10274407	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10279308	0.91[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs1043466	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10953286	0.88[GIH][hapmap];1.00[YRI][hapmap]
rs10953287	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11762273	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]
rs11771702	0.83[CEU][hapmap]
rs11772470	0.83[JPT][hapmap]
rs11973460	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11976018	0.91[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs11978089	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs12112936	0.83[CEU][hapmap]
rs12113440	0.83[CEU][hapmap]
rs13227795	0.80[AMR][1000 genomes]
rs13240600	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs17161695	0.83[CEU][hapmap]
rs17161698	0.85[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1980307	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs1985453	0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs2003499	0.91[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2057905	0.81[ASN][1000 genomes]
rs2057906	0.84[ASN][1000 genomes]
rs2072181	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[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107922	0.88[EUR][1000 genomes]
rs2240384	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2269985	0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2272168	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs2280600	0.83[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2280601	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2286162	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2404322	0.83[ASN][1000 genomes]
rs2404323	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404324	0.95[AFR][1000 genomes]
rs28457808	0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs28495024	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28820905	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3137	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs3764815	0.82[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3779354	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs3801288	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3843540	0.83[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs4729532	0.92[ASW][hapmap];0.91[CEU][hapmap];0.81[MKK][hapmap]
rs59986060	0.81[ASN][1000 genomes]
rs6943920	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6953476	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6955490	0.92[ASW][hapmap];0.91[CEU][hapmap];0.81[MKK][hapmap];0.82[EUR][1000 genomes]
rs6961634	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs6962772	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs6972337	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6975099	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs733991	0.83[CEU][hapmap]
rs7794682	0.80[AMR][1000 genomes]
rs7794705	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs883403	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs917154	0.91[ASW][hapmap];0.91[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9641253	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9768020	0.87[AMR][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
rs10243678	ARPC1B	cis	Thyroid	GTEx
rs10243678	ZKSCAN1	cis	parietal	SCAN
rs10243678	PILRA	cis	cerebellum	SCAN
rs10243678	OR2AE1	cis	parietal	SCAN
rs10243678	CPSF4	cis	parietal	SCAN
rs10243678	ACTL6B	cis	cerebellum	SCAN
rs10243678	GATS	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98979400-99001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:98980400-99003800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:98980800-99000600	Strong transcription	Dnd41	blood
4	chr7:98981000-98993000	Strong transcription	A549	lung
5	chr7:98985600-99003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:98986200-98992000	Weak transcription	HSMMtube	muscle
7	chr7:98987000-99004200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:98989800-98992000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:98990000-98992000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:98990000-99002800	Strong transcription	GM12878-XiMat	blood
11	chr7:98990200-98994600	Weak transcription	NHDF-Ad	bronchial
12	chr7:98990800-98992400	Weak transcription	Hela-S3	cervix
13	chr7:98991000-98992000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr7:98991000-98992200	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr7:98991000-98992200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:98991000-98993200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:98991000-98995000	Weak transcription	Aorta	Aorta
18	chr7:98991000-98996200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr7:98991000-99001600	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr7:98991000-99001600	Strong transcription	Osteobl	bone
21	chr7:98991000-99002000	Strong transcription	NHEK	skin
22	chr7:98991000-99002600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr7:98991000-99002600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:98991200-98992000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr7:98991200-98992000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:98991200-98992000	Genic enhancers	Fetal Thymus	thymus
27	chr7:98991200-98992200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr7:98991200-98993800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:98991200-98996400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:98991200-98996600	Strong transcription	HSMM	muscle
31	chr7:98991400-98992000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr7:98991400-98992000	Weak transcription	Brain Substantia Nigra	brain
33	chr7:98991400-98992000	Genic enhancers	Fetal Intestine Large	intestine
34	chr7:98991400-98992000	Genic enhancers	Fetal Stomach	stomach
35	chr7:98991400-98992000	Genic enhancers	Left Ventricle	heart
36	chr7:98991400-98992000	Enhancers	Psoas Muscle	Psoas
37	chr7:98991400-98992000	Genic enhancers	Rectal Mucosa Donor 29	rectum
38	chr7:98991400-98992400	Weak transcription	Brain Anterior Caudate	brain
39	chr7:98991400-98993600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:98991400-98994200	Weak transcription	Ovary	ovary
41	chr7:98991400-98995400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:98991400-99001800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:98991400-99001800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:98991400-99001800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr7:98991400-99002400	Strong transcription	Esophagus	oesophagus
46	chr7:98991400-99002400	Weak transcription	Right Atrium	heart
47	chr7:98991400-99004200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr7:98991600-98992000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:98991600-98992000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr7:98991600-98992000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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