Variant report

Variant	rs2301257
Chromosome Location	chr7:150555547-150555548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10234348	0.86[JPT][hapmap]
rs10236489	0.82[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10250599	0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10280024	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1049793	0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10893	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10952294	0.92[ASN][1000 genomes]
rs11971392	0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs11971459	0.90[ASN][1000 genomes]
rs11978239	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12179	0.92[ASN][1000 genomes]
rs12703105	0.82[JPT][hapmap]
rs2071514	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2071515	0.92[ASN][1000 genomes]
rs2071517	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34459590	0.90[ASN][1000 genomes]
rs35573300	0.81[ASN][1000 genomes]
rs3735076	0.92[ASN][1000 genomes]
rs4725968	0.92[ASN][1000 genomes]
rs4725972	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2758140	chr7:150538821-150663697	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2759574	chr7:150538821-150663697	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1031497	chr7:150547113-150572570	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1029395	chr7:150547113-150574552	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1028241	chr7:150552873-150572570	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv32879	chr7:150553149-150573695	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv2755450	chr7:150553352-150572352	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv608993	chr7:150553475-150560322	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv608994	chr7:150553475-150568581	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv608995	chr7:150553475-150572382	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv608996	chr7:150553605-150572382	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv1020449	chr7:150553745-150572570	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	esv2761383	chr7:150553757-150560322	Weak transcription Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2301257	XRCC2	cis	cerebellum	SCAN
rs2301257	TMEM176A	cis	parietal	SCAN
rs2301257	ZNF767	cis	cerebellum	SCAN
rs2301257	TMEM176B	cis	cerebellum	SCAN
rs2301257	ABCB8	cis	cerebellum	SCAN
rs2301257	C7orf33	cis	parietal	SCAN
rs2301257	TMEM176B	cis	parietal	SCAN
rs2301257	RHEB	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150543200-150557600	Weak transcription	Right Atrium	heart
2	chr7:150549800-150557400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:150549800-150558400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:150550000-150557400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:150553200-150558800	Strong transcription	Fetal Intestine Small	intestine
6	chr7:150553600-150558800	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr7:150553600-150559400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr7:150553800-150556400	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:150553800-150557400	Weak transcription	Spleen	Spleen
10	chr7:150553800-150558600	Strong transcription	Fetal Intestine Large	intestine
11	chr7:150554000-150556200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:150554800-150555800	Weak transcription	Colonic Mucosa	Colon
13	chr7:150555000-150561400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr7:150555200-150556200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:150555400-150556000	Bivalent Enhancer	Placenta	Placenta
16	chr7:150555400-150564000	Weak transcription	Liver	Liver

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