Variant report

Variant	rs7898249
Chromosome Location	chr10:116709223-116709224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:116697261..116699951-chr10:116709059..116711441,4	MCF-7	breast:
2	chr10:116708122..116710473-chr10:116713973..116715764,2	MCF-7	breast:
3	chr10:116695542..116700856-chr10:116705111..116709890,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165832	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10160015	0.95[ASN][1000 genomes]
rs10444099	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10490908	1.00[JPT][hapmap]
rs10510008	0.86[ASN][1000 genomes]
rs10885631	0.82[ASN][1000 genomes]
rs10885632	0.86[ASN][1000 genomes]
rs10885633	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885634	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885636	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10885637	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10885638	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10885639	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196983	0.86[ASN][1000 genomes]
rs11196984	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11196989	0.86[ASN][1000 genomes]
rs11196991	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196996	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196999	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197000	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11197007	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197010	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11197011	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11197012	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11197023	0.95[ASN][1000 genomes]
rs12098332	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12246008	0.95[ASN][1000 genomes]
rs12265048	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12269261	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12764662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12772737	0.95[ASN][1000 genomes]
rs12774597	0.95[ASN][1000 genomes]
rs12775180	1.00[JPT][hapmap]
rs12779231	0.95[ASN][1000 genomes]
rs17092542	1.00[JPT][hapmap]
rs17721283	1.00[JPT][hapmap]
rs17721905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17722042	0.95[ASN][1000 genomes]
rs17794346	1.00[JPT][hapmap]
rs17795104	0.95[ASN][1000 genomes]
rs17795212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1966384	1.00[JPT][hapmap]
rs2095379	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105001	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420070	0.86[ASN][1000 genomes]
rs34170154	0.95[ASN][1000 genomes]
rs34434610	0.95[ASN][1000 genomes]
rs34453431	0.95[ASN][1000 genomes]
rs34461950	0.87[ASN][1000 genomes]
rs35501899	0.95[ASN][1000 genomes]
rs35811923	0.95[ASN][1000 genomes]
rs3931556	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869271	0.95[ASN][1000 genomes]
rs61869272	0.95[ASN][1000 genomes]
rs61869274	0.95[ASN][1000 genomes]
rs61869275	0.95[ASN][1000 genomes]
rs6585302	0.86[ASN][1000 genomes]
rs6585306	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585309	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6585310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6585311	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6585313	0.95[ASN][1000 genomes]
rs7071789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7071812	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7072356	1.00[JPT][hapmap]
rs7074729	1.00[JPT][hapmap]
rs7075888	1.00[JPT][hapmap]
rs7079234	0.95[ASN][1000 genomes]
rs7085964	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7093282	0.83[ASN][1000 genomes]
rs7093330	0.95[ASN][1000 genomes]
rs7094072	1.00[JPT][hapmap]
rs7097580	0.95[ASN][1000 genomes]
rs7099565	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7099590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7099779	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7100159	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100894	0.86[ASN][1000 genomes]
rs72836518	0.95[ASN][1000 genomes]
rs749649	1.00[JPT][hapmap]
rs7895551	1.00[JPT][hapmap]
rs7904605	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908069	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7908464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909566	1.00[JPT][hapmap]
rs7909657	1.00[JPT][hapmap]
rs7917523	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923295	1.00[JPT][hapmap]
rs881192	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968848	0.95[ASN][1000 genomes]
rs968849	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv831997	chr10:116689552-116855698	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7898249	LOC143188	cis	parietal	SCAN
rs7898249	ARHGAP6	trans	cerebellum	SCAN
rs7898249	SHOC2	cis	parietal	SCAN
rs7898249	TECTB	cis	cerebellum	SCAN
rs7898249	TRUB1	Cis_1M	lymphoblastoid	RTeQTL
rs7898249	ATRNL1	cis	Muscle Skeletal	GTEx
rs7898249	TRUB1	cis	cerebellum	SCAN
rs7898249	ADRB1	cis	parietal	SCAN
rs7898249	TRUB1	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116698800-116730400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:116698800-116763600	Weak transcription	Esophagus	oesophagus
3	chr10:116699200-116722400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:116699200-116722600	Weak transcription	Aorta	Aorta
5	chr10:116699600-116736400	Weak transcription	NHLF	lung
6	chr10:116699800-116722400	Weak transcription	Fetal Kidney	kidney
7	chr10:116699800-116726200	Weak transcription	K562	blood
8	chr10:116700200-116714800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:116700600-116716000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:116700800-116709400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr10:116700800-116709400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:116700800-116709600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr10:116700800-116709800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:116700800-116713000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr10:116700800-116722600	Weak transcription	Fetal Brain Male	brain
16	chr10:116701000-116715000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr10:116701200-116716200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:116701600-116713800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr10:116702000-116710800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr10:116702400-116709400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:116702400-116715200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:116702400-116716000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:116703400-116730400	Weak transcription	Pancreas	Pancrea
24	chr10:116703600-116710400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr10:116703600-116714600	Weak transcription	Colon Smooth Muscle	Colon
26	chr10:116703600-116715200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr10:116703600-116716800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr10:116703600-116717000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr10:116703600-116722200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr10:116703600-116722400	Weak transcription	Gastric	stomach
31	chr10:116703600-116722400	Weak transcription	Lung	lung
32	chr10:116703600-116722400	Weak transcription	Spleen	Spleen
33	chr10:116703600-116722600	Weak transcription	Brain Substantia Nigra	brain
34	chr10:116703600-116740800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr10:116703600-116747800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr10:116704000-116713400	Weak transcription	Psoas Muscle	Psoas
37	chr10:116704000-116722000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr10:116704600-116709600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr10:116705000-116728000	Weak transcription	Small Intestine	intestine
40	chr10:116705200-116721800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:116705400-116711400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr10:116705400-116713400	Weak transcription	Brain Germinal Matrix	brain
43	chr10:116705400-116713400	Weak transcription	Left Ventricle	heart
44	chr10:116705400-116714400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr10:116705400-116717200	Weak transcription	Right Ventricle	heart
46	chr10:116705400-116722200	Weak transcription	Fetal Brain Female	brain
47	chr10:116705400-116735400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr10:116705400-116739400	Weak transcription	Thymus	Thymus
49	chr10:116705600-116711400	Weak transcription	Primary B cells from cord blood	blood
50	chr10:116705600-116712000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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