Variant report

Variant	rs10282458
Chromosome Location	chr7:150045302-150045303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150006854..150009038-chr7:150044766..150046697,2	MCF-7	breast:
2	chr7:150037012..150039483-chr7:150043984..150046592,2	K562	blood:
3	chr7:150043043..150045411-chr7:150065922..150068043,3	K562	blood:
4	chr7:150036951..150040466-chr7:150042649..150046441,3	MCF-7	breast:
5	chr7:150027400..150032062-chr7:150042687..150047814,5	K562	blood:

Variant related genes	Relation type
ENSG00000261305	Chromatin interaction
ENSG00000214022	Chromatin interaction
ENSG00000106538	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10248490	0.87[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10259796	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1047207	0.91[EUR][1000 genomes]
rs1047575	0.84[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1047586	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1051760	0.90[CEU][hapmap]
rs1051764	0.90[CEU][hapmap]
rs1051823	0.89[CEU][hapmap]
rs10952250	0.90[CEU][hapmap];0.83[TSI][hapmap]
rs10952252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132261	0.90[CEU][hapmap]
rs11764936	0.90[CEU][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs11765644	0.85[EUR][1000 genomes]
rs11767409	0.90[ASN][1000 genomes]
rs11769348	0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11773351	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13223702	0.90[ASN][1000 genomes]
rs17173617	0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs17173681	0.95[CEU][hapmap]
rs17173682	0.95[CEU][hapmap]
rs1962004	0.82[EUR][1000 genomes]
rs1983440	0.90[CEU][hapmap]
rs2098053	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2159236	0.81[CEU][hapmap]
rs2373751	0.85[EUR][1000 genomes]
rs28432021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28439010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088207	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34489187	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34495356	0.90[ASN][1000 genomes]
rs34728606	0.94[ASN][1000 genomes]
rs36035506	0.90[ASN][1000 genomes]
rs3735167	0.95[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3735169	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3735170	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3735171	0.94[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3735172	0.90[CEU][hapmap];0.83[TSI][hapmap]
rs3757423	0.90[CEU][hapmap]
rs3757425	0.90[CEU][hapmap]
rs3800780	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3800781	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4395803	0.85[EUR][1000 genomes]
rs4554381	0.90[CEU][hapmap]
rs55881542	0.85[EUR][1000 genomes]
rs55974958	0.91[EUR][1000 genomes]
rs56190213	0.85[EUR][1000 genomes]
rs61421252	0.91[EUR][1000 genomes]
rs66688634	0.94[ASN][1000 genomes]
rs6722	0.89[CEU][hapmap]
rs68107602	0.80[EUR][1000 genomes]
rs6946097	0.90[CEU][hapmap]
rs6964110	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73170185	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73170192	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7800196	0.95[CEU][hapmap]
rs883138	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv508490	chr7:150006068-150051241	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv889453	chr7:150009838-150104410	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers 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 target site	50 gene(s)	inside rSNPs	diseases
6	nsv889454	chr7:150009838-150115183	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv889455	chr7:150013393-150104410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv889456	chr7:150013393-150115183	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
9	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
11	nsv889457	chr7:150020295-150104410	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription 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 target site	50 gene(s)	inside rSNPs	diseases
12	nsv889458	chr7:150020295-150115183	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
13	nsv521407	chr7:150020295-150118590	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
14	nsv465211	chr7:150035526-150104410	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
15	nsv608991	chr7:150035526-150104410	Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
16	nsv889459	chr7:150041610-150071464	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs10282458	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs10282458	RP4-584D14.7	cis	Nerve Tibial	GTEx
rs10282458	RARRES2	cis	multi-tissue	Pritchard
rs10282458	C7orf29	cis	multi-tissue	Pritchard
rs10282458	RARRES2	cis	lymphoblastoid	seeQTL
rs10282458	C7orf29	cis	cerebellum	SCAN
rs10282458	LRRC61	cis	Esophagus Mucosa	GTEx
rs10282458	RARRES2	trans	brain	seeQTL
rs10282458	LRRC61	cis	lymphoblastoid	seeQTL
rs10282458	ACTR3C	cis	Muscle Skeletal	GTEx
rs10282458	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs10282458	LRRC61	cis	parietal	SCAN
rs10282458	C7orf29	cis	lymphoblastoid	seeQTL
rs10282458	RARRES2	cis	brain	seeQTL
rs10282458	LRRC61	cis	Thyroid	GTEx
rs10282458	LRRC61	cis	lung	GTEx
rs10282458	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs10282458	GIMAP6	cis	cerebellum	SCAN
rs10282458	LRRC61	cis	Nerve Tibial	GTEx
rs10282458	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs10282458	LRRC61	cis	Adipose Subcutaneous	GTEx
rs10282458	LRRC61	cis	Artery Tibial	GTEx
rs10282458	REPIN1	cis	Muscle Skeletal	GTEx
rs10282458	MGC3036	cis	multi-tissue	Pritchard
rs10282458	LRRC61	cis	cerebellum	SCAN
rs10282458	LRRC61	cis	Whole Blood	GTEx
rs10282458	LRRC61	cis	Muscle Skeletal	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150038800-150052600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:150039200-150065000	Weak transcription	Right Atrium	heart
3	chr7:150039600-150046200	Weak transcription	Ovary	ovary
4	chr7:150041200-150051200	Weak transcription	HepG2	liver
5	chr7:150042000-150052400	Weak transcription	Dnd41	blood
6	chr7:150044000-150058000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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