Variant report

Variant	rs10271869
Chromosome Location	chr7:150052988-150052989
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	chr7:150018896..150021417-chr7:150052891..150055255,2	MCF-7	breast:
3	chr7:150043135..150045131-chr7:150050949..150053058,2	MCF-7	breast:
4	chr7:150019173..150023075-chr7:150052530..150058157,7	K562	blood:

Variant related genes	Relation type
ENSG00000127399	Chromatin interaction
ENSG00000106526	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10248975	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10264443	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10278277	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051760	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1051764	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1051823	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10952251	0.94[ASN][1000 genomes]
rs11771677	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771693	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972067	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1983441	0.84[EUR][1000 genomes]
rs28398138	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3735165	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3735166	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757423	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757424	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757425	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6722	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6946097	0.86[EUR][1000 genomes]
rs6946153	0.86[EUR][1000 genomes]
rs71537958	0.85[EUR][1000 genomes]
rs7800196	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9640161	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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10271869	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs10271869	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs10271869	LRRC61	cis	Adipose Subcutaneous	GTEx
rs10271869	LRRC61	cis	Artery Aorta	GTEx
rs10271869	LRRC61	cis	Muscle Skeletal	GTEx
rs10271869	REPIN1	cis	Muscle Skeletal	GTEx
rs10271869	C7orf29	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150039200-150065000	Weak transcription	Right Atrium	heart
2	chr7:150044000-150058000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:150049000-150053400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:150049400-150053800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:150049600-150054400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:150049800-150054600	Weak transcription	Placenta	Placenta
7	chr7:150051200-150056600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:150051400-150053000	Enhancers	Rectal Smooth Muscle	rectum
9	chr7:150051400-150054400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:150051600-150053400	Enhancers	Colon Smooth Muscle	Colon
11	chr7:150052000-150053000	Enhancers	Colonic Mucosa	Colon
12	chr7:150052000-150053000	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr7:150052000-150061000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr7:150052200-150053400	Enhancers	Stomach Mucosa	stomach
15	chr7:150052200-150056600	Enhancers	Primary hematopoietic stem cells	blood
16	chr7:150052400-150053000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr7:150052400-150053000	Enhancers	Fetal Kidney	kidney
18	chr7:150052400-150053000	Flanking Active TSS	HepG2	liver
19	chr7:150052400-150053200	Enhancers	Thymus	Thymus
20	chr7:150052400-150053800	Enhancers	Dnd41	blood
21	chr7:150052400-150054400	Enhancers	GM12878-XiMat	blood
22	chr7:150052400-150054800	Enhancers	K562	blood
23	chr7:150052400-150055200	Enhancers	Adipose Nuclei	Adipose
24	chr7:150052600-150053000	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr7:150052600-150053200	Enhancers	A549	lung
26	chr7:150052600-150054600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr7:150052600-150054800	Enhancers	Liver	Liver
28	chr7:150052800-150053200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr7:150052800-150053200	Weak transcription	Fetal Thymus	thymus
30	chr7:150052800-150053600	Enhancers	Stomach Smooth Muscle	stomach
31	chr7:150052800-150053800	Weak transcription	Duodenum Mucosa	Duodenum

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