Variant report

Variant	rs34728606
Chromosome Location	chr7:150054694-150054695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:150018896..150021417-chr7:150052891..150055255,2	MCF-7	breast:
2	chr7:150025962..150028833-chr7:150053368..150055089,2	K562	blood:
3	chr7:150054480..150054997-chr7:150114557..150115424,2	K562	blood:
4	chr7:150009132..150011651-chr7:150053831..150057388,3	K562	blood:
5	chr7:150054220..150054841-chr7:150074964..150075932,2	K562	blood:
6	chr7:150019173..150023075-chr7:150052530..150058157,7	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC61-2	chr7:150054392-150055006	XLOC_006291
2	lnc-LRRC61-2	chr7:150054388-150055176	NONHSAT124108

No data

Variant related genes	Relation type
ENSG00000188707	Chromatin interaction
ENSG00000106526	Chromatin interaction
ENSG00000127399	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10248490	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10259796	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10282458	0.94[ASN][1000 genomes]
rs10952252	0.94[ASN][1000 genomes]
rs1132261	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11766288	0.87[AFR][1000 genomes]
rs11767409	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11768108	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11773351	0.81[AFR][1000 genomes]
rs12703061	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13223702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13238964	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13307276	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17173681	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17173682	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17173702	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17173703	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2098053	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2373751	0.87[AFR][1000 genomes]
rs28432021	0.94[ASN][1000 genomes]
rs28439010	0.94[ASN][1000 genomes]
rs34311995	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34489187	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34495356	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35435439	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35635199	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35840727	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36035506	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36069544	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3735167	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs56190213	0.81[AFR][1000 genomes]
rs56402329	0.87[AFR][1000 genomes]
rs57888387	0.87[AFR][1000 genomes]
rs66688634	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68107602	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6946097	0.80[AMR][1000 genomes]
rs6946153	0.80[AMR][1000 genomes]
rs6964110	0.87[ASN][1000 genomes]
rs71537957	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73170169	0.87[AFR][1000 genomes]
rs73170192	0.86[ASN][1000 genomes]
rs7800196	0.83[EUR][1000 genomes]
rs883138	0.87[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs34728606	LRRC61	cis	Nerve Tibial	GTEx
rs34728606	LRRC61	cis	Thyroid	GTEx
rs34728606	LRRC61	cis	Esophagus Mucosa	GTEx
rs34728606	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs34728606	REPIN1	cis	Muscle Skeletal	GTEx
rs34728606	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs34728606	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs34728606	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs34728606	LRRC61	cis	Muscle Skeletal	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

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	chr7:150051200-150056600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:150052000-150061000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr7:150052200-150056600	Enhancers	Primary hematopoietic stem cells	blood
6	chr7:150052400-150054800	Enhancers	K562	blood
7	chr7:150052400-150055200	Enhancers	Adipose Nuclei	Adipose
8	chr7:150052600-150054800	Enhancers	Liver	Liver
9	chr7:150053000-150056400	Weak transcription	Fetal Kidney	kidney
10	chr7:150053000-150058000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:150053000-150058400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:150053200-150055200	Enhancers	Primary B cells from peripheral blood	blood
13	chr7:150053200-150065000	Enhancers	Fetal Thymus	thymus
14	chr7:150053400-150056400	Enhancers	Primary T cells from cord blood	blood
15	chr7:150053400-150056400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:150053400-150056600	Enhancers	Primary T cells fromperipheralblood	blood
17	chr7:150053600-150055200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr7:150053600-150055200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:150053800-150054800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr7:150053800-150055200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:150053800-150055200	Enhancers	Duodenum Mucosa	Duodenum
22	chr7:150053800-150055200	Flanking Active TSS	Dnd41	blood
23	chr7:150053800-150055400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr7:150053800-150055400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr7:150053800-150055400	Enhancers	HSMMtube	muscle
26	chr7:150053800-150055600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr7:150053800-150056800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr7:150054200-150055200	Enhancers	Primary B cells from cord blood	blood
29	chr7:150054200-150055400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:150054200-150056800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:150054400-150054800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr7:150054400-150054800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:150054400-150054800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr7:150054400-150054800	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr7:150054400-150054800	Flanking Active TSS	GM12878-XiMat	blood
36	chr7:150054400-150054800	Flanking Active TSS	HSMM	muscle
37	chr7:150054400-150055000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr7:150054400-150055000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr7:150054400-150055000	Enhancers	A549	lung
40	chr7:150054400-150055000	Flanking Active TSS	HepG2	liver
41	chr7:150054400-150055200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr7:150054400-150055200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:150054400-150055200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr7:150054400-150055200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr7:150054400-150055200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr7:150054400-150055200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr7:150054400-150055200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:150054400-150055200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr7:150054400-150055200	Enhancers	Spleen	Spleen
50	chr7:150054400-150055400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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