Variant report

Variant	rs10237343
Chromosome Location	chr7:102049757-102049758
allele	C/G
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:5)
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	RUNX3	chr7:102049505-102049888	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:102049687-102050165	GM12878	blood:	n/a	n/a
3	NFIC	chr7:102049481-102049863	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:102034801..102038822-chr7:102042441..102049946,10	MCF-7	breast:
2	chr7:102049708..102051237-chr7:102053015..102054788,2	K562	blood:
3	chr7:102048214..102051308-chr7:102051433..102054788,6	K562	blood:
4	chr7:102047341..102050433-chr7:102088256..102090281,3	MCF-7	breast:
5	chr7:102048352..102050476-chr7:102073895..102075585,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR548O	TF binding region
ENSG00000128563	Chromatin interaction
ENSG00000160991	Chromatin interaction
ENSG00000239480	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10225683	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10226565	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10233236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10233461	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10235407	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10238685	0.84[ASW][hapmap]
rs10239657	0.84[EUR][1000 genomes]
rs10243209	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10246324	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10249217	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10249222	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10249581	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10255036	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10268289	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10268970	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10276094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10277996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10278274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11982980	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11983129	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12672132	0.83[EUR][1000 genomes]
rs17135197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1983476	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1997164	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2103229	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2410990	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2411005	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28427402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28539797	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28879187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4481505	0.81[EUR][1000 genomes]
rs4729789	0.81[EUR][1000 genomes]
rs56295031	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6465859	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6947435	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6951185	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6953087	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6958795	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6968325	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6970496	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6974177	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7384178	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7385200	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7787493	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9632724	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1814780	chr7:101912320-102375950	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv1819566	chr7:101912320-102375950	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Enhancers Genic enhancers 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1822347	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv1825708	chr7:101912320-102375950	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	esv1842898	chr7:101912320-102375950	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	esv1847418	chr7:101912320-102375950	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv427798	chr7:101912320-102375950	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv428182	chr7:101912320-102375950	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
10	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
11	nsv1029079	chr7:101939998-102112371	Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
12	esv1818954	chr7:101957513-102328097	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	esv1828190	chr7:101966669-102439077	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
14	esv1829377	chr7:101970299-102330884	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv831083	chr7:101981005-102295869	Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
16	esv1806297	chr7:101981544-102330884	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
17	esv1810415	chr7:101993063-102375950	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	esv1811751	chr7:101993063-102375950	Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
19	esv1829118	chr7:101993063-102375950	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
20	esv1833155	chr7:101993063-102375950	Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10237343	AGFG2	cis	parietal	SCAN
rs10237343	POLR2J	cis	multi-tissue	Pritchard
rs10237343	PMS2L3	trans	multi-tissue	Pritchard
rs10237343	C7orf19	cis	multi-tissue	Pritchard
rs10237343	ORAI2	cis	Whole Blood	GTEx
rs10237343	PRKRIP1	cis	multi-tissue	Pritchard
rs10237343	MEPCE	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102037800-102051400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:102038000-102049800	Weak transcription	Psoas Muscle	Psoas
3	chr7:102038000-102066800	Weak transcription	Stomach Mucosa	stomach
4	chr7:102038400-102049800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:102038400-102055600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:102038600-102049800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr7:102038800-102050400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:102038800-102053000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:102038800-102053000	Strong transcription	Thymus	Thymus
10	chr7:102038800-102054000	Strong transcription	Primary T cells from cord blood	blood
11	chr7:102038800-102068600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:102039000-102050400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:102039000-102054000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:102039000-102055000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr7:102039000-102058000	Strong transcription	Osteobl	bone
16	chr7:102039000-102062400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:102039000-102062400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr7:102039200-102049800	Strong transcription	Fetal Intestine Small	intestine
19	chr7:102039200-102049800	Strong transcription	Fetal Muscle Leg	muscle
20	chr7:102039200-102050400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr7:102039200-102050400	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr7:102039200-102051000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:102039200-102051000	Strong transcription	HSMMtube	muscle
24	chr7:102039200-102053000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:102039200-102053200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr7:102039200-102053800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:102039200-102057200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:102039200-102059200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr7:102039200-102059800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr7:102039200-102062400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr7:102039200-102062600	Strong transcription	Dnd41	blood
32	chr7:102039200-102068200	Strong transcription	Placenta	Placenta
33	chr7:102039200-102070000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:102039400-102049800	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr7:102039400-102060200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr7:102039400-102060600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr7:102039400-102061000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr7:102039400-102061600	Strong transcription	Fetal Intestine Large	intestine
39	chr7:102039400-102063000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:102039400-102063600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:102039600-102051000	Strong transcription	Fetal Brain Female	brain
42	chr7:102039600-102051200	Strong transcription	Rectal Smooth Muscle	rectum
43	chr7:102039600-102052600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:102039600-102053200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr7:102039600-102060000	Strong transcription	Fetal Lung	lung
46	chr7:102039600-102067800	Strong transcription	Liver	Liver
47	chr7:102039600-102068200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr7:102039800-102050200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr7:102039800-102050400	Strong transcription	Lung	lung
50	chr7:102039800-102051000	Strong transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links