Variant report

Variant	rs10259796
Chromosome Location	chr7:150050427-150050428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150019092..150022415-chr7:150049163..150053845,5	K562	blood:
2	chr7:150027884..150030451-chr7:150047848..150050631,2	K562	blood:
3	chr7:150047669..150050578-chr7:150054703..150056405,2	MCF-7	breast:
4	chr7:150019297..150022002-chr7:150048470..150050595,2	MCF-7	breast:
5	chr7:150047990..150050498-chr7:150066591..150069127,2	K562	blood:
6	chr7:150019828..150022176-chr7:150049163..150051889,2	K562	blood:
7	chr7:150048612..150050874-chr7:150063733..150065567,2	K562	blood:

Variant related genes	Relation type
ENSG00000127399	Chromatin interaction
ENSG00000214022	Chromatin interaction
ENSG00000106526	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10248490	0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10263486	0.85[YRI][hapmap]
rs10282458	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1047575	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1051760	0.85[CEU][hapmap]
rs1051764	0.85[CEU][hapmap]
rs1051823	0.80[CEU][hapmap]
rs10952250	0.85[CEU][hapmap]
rs10952252	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1132261	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11764936	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs11767409	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11768108	0.86[EUR][1000 genomes]
rs11769348	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12703061	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13223702	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13238964	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13307276	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17173617	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs17173681	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17173682	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17173702	0.85[EUR][1000 genomes]
rs17173703	0.85[EUR][1000 genomes]
rs1983440	0.85[CEU][hapmap]
rs2098053	0.90[ASN][1000 genomes]
rs28432021	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28439010	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34311995	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34489187	0.95[ASN][1000 genomes]
rs34495356	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34728606	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35435439	0.86[EUR][1000 genomes]
rs35635199	0.86[EUR][1000 genomes]
rs35840727	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36035506	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36069544	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3735167	0.90[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3735169	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs3735170	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs3735171	0.94[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap]
rs3735172	0.85[CEU][hapmap]
rs3757423	0.85[CEU][hapmap]
rs3757425	0.81[CEU][hapmap]
rs4554381	0.85[CEU][hapmap]
rs66688634	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6722	0.84[CEU][hapmap]
rs68107602	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6946097	0.81[CEU][hapmap]
rs6964110	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs71537957	0.84[EUR][1000 genomes]
rs73170192	0.88[ASN][1000 genomes]
rs7800196	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs883138	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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
17	nsv608992	chr7:150045910-150115183	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10259796	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs10259796	RARRES2	cis	multi-tissue	Pritchard
rs10259796	ACTR3C	cis	Muscle Skeletal	GTEx
rs10259796	REPIN1	cis	Muscle Skeletal	GTEx
rs10259796	LRRC61	cis	Muscle Skeletal	GTEx
rs10259796	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs10259796	LRRC61	cis	Thyroid	GTEx
rs10259796	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs10259796	LRRC61	cis	Nerve Tibial	GTEx
rs10259796	C7orf29	cis	multi-tissue	Pritchard
rs10259796	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:13 , 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	chr7:150041200-150051200	Weak transcription	HepG2	liver
4	chr7:150042000-150052400	Weak transcription	Dnd41	blood
5	chr7:150044000-150058000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:150049000-150053400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:150049400-150053800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:150049600-150052000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr7:150049600-150052400	Weak transcription	K562	blood
10	chr7:150049600-150052600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr7:150049600-150052600	Weak transcription	A549	lung
12	chr7:150049600-150054400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:150049800-150054600	Weak transcription	Placenta	Placenta

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