Variant report

Variant	rs10951255
Chromosome Location	chr7:3631115-3631116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10245071	1.00[CHD][hapmap]
rs10951207	1.00[ASW][hapmap];0.86[MEX][hapmap]
rs10951254	0.82[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs10951265	1.00[YRI][hapmap]
rs11765058	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11768609	0.82[MEX][hapmap]
rs11770829	1.00[YRI][hapmap]
rs12531560	1.00[YRI][hapmap]
rs12531698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12539805	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs12540148	1.00[YRI][hapmap]
rs12701005	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13223065	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13223852	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13240060	1.00[YRI][hapmap]
rs13240393	0.82[ASN][1000 genomes]
rs13242531	0.90[MEX][hapmap];0.85[YRI][hapmap]
rs1522502	1.00[YRI][hapmap]
rs1922016	1.00[YRI][hapmap]
rs2099302	0.90[MEX][hapmap]
rs2341584	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2341585	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341586	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2614970	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2705604	0.97[ASN][1000 genomes]
rs2705609	1.00[ASW][hapmap]
rs2705612	0.93[ASN][1000 genomes]
rs34008696	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34015199	0.90[ASN][1000 genomes]
rs34024103	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34227479	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34703718	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34704704	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34872052	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34953429	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35453716	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35669868	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3919653	0.81[MEX][hapmap]
rs4342491	0.86[MEX][hapmap]
rs4722903	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs4722951	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs62437874	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62440182	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73037689	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs956393	0.90[MEX][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap]
rs9648355	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv916071	chr7:3423207-3697428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv887334	chr7:3531275-3635105	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1023888	chr7:3539750-3638242	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1034298	chr7:3539750-3646251	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv830888	chr7:3577214-3776276	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv1792280	chr7:3592290-3668229	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1017012	chr7:3602397-3638242	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv538679	chr7:3602397-3638242	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv605909	chr7:3605340-3638547	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv2752641	chr7:3609495-3631115	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv2752926	chr7:3609712-3631115	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv2754251	chr7:3609712-3631115	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv948390	chr7:3609821-3734421	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv1033415	chr7:3616095-3753563	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv538680	chr7:3616095-3753563	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv1016930	chr7:3627295-3705057	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv530553	chr7:3629504-3736851	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10951255	MXRA5	trans	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3625800-3631200	Weak transcription	Stomach Mucosa	stomach
2	chr7:3625800-3631400	Weak transcription	Brain Germinal Matrix	brain
3	chr7:3625800-3631600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:3625800-3632200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:3625800-3632600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:3626600-3632200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:3629600-3632200	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:3629600-3632200	Weak transcription	Pancreas	Pancrea
9	chr7:3630400-3633400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr7:3630600-3632800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr7:3630800-3632800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr7:3630800-3633200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:3630800-3633400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:3630800-3633400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr7:3631000-3631200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr7:3631000-3631200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:3631000-3632200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:3631000-3632400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr7:3631000-3632800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr7:3631000-3632800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr7:3631000-3633200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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