Variant report

Variant	rs3735167
Chromosome Location	chr7:150039555-150039556
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150038539..150040315-chr7:150063994..150067487,3	MCF-7	breast:
2	chr7:150019150..150025305-chr7:150035524..150043799,10	MCF-7	breast:
3	chr7:150018389..150025798-chr7:150030734..150040389,17	MCF-7	breast:
4	chr7:150025602..150029595-chr7:150039104..150043017,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC61-1	chr7:150038860-150039696	ENSG00000261305.1

Variant related genes	Relation type
ENSG00000127399	Chromatin interaction
ENSG00000188707	Chromatin interaction
ENSG00000196456	Chromatin interaction
ENSG00000214022	Chromatin interaction
ENSG00000106526	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10248490	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10259796	0.90[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10282458	0.95[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1047207	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1047575	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1047586	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1051760	0.84[CEU][hapmap]
rs1051764	0.84[CEU][hapmap]
rs1051823	0.84[CEU][hapmap]
rs10952250	0.95[CEU][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs10952252	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1132261	0.84[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes]
rs11764936	0.95[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11765644	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11765692	0.85[EUR][1000 genomes]
rs11766288	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11767726	0.84[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11769348	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11773351	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11974980	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs11983355	0.82[EUR][1000 genomes]
rs13223702	0.87[AFR][1000 genomes]
rs1464752	0.83[EUR][1000 genomes]
rs1464753	0.85[EUR][1000 genomes]
rs17173617	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17173681	0.84[ASW][hapmap];0.89[CEU][hapmap]
rs17173682	0.84[ASW][hapmap];0.89[CEU][hapmap]
rs17837498	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs1916932	0.85[EUR][1000 genomes]
rs1962004	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1983440	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2098053	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108851	0.82[EUR][1000 genomes]
rs2108852	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2108853	0.82[EUR][1000 genomes]
rs2108854	0.84[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs2159234	0.82[EUR][1000 genomes]
rs2159235	0.82[EUR][1000 genomes]
rs2159236	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2373751	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28432021	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28439010	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3088207	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34489187	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34728606	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs36069544	0.81[AFR][1000 genomes]
rs3735169	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3735170	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3735171	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3735172	0.95[CEU][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs3735173	0.83[EUR][1000 genomes]
rs3735174	0.83[EUR][1000 genomes]
rs3735175	0.82[EUR][1000 genomes]
rs3757423	0.84[CEU][hapmap]
rs3757425	0.84[CEU][hapmap]
rs3800780	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800781	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4395803	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4554381	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs55881542	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55974958	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56190213	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56402329	1.00[AFR][1000 genomes]
rs57888387	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60268791	0.84[EUR][1000 genomes]
rs60283368	0.85[EUR][1000 genomes]
rs61421252	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66688634	0.83[ASN][1000 genomes]
rs6722	0.83[CEU][hapmap]
rs6946097	0.84[CEU][hapmap]
rs6964110	0.95[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73170169	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73170174	0.82[EUR][1000 genomes]
rs73170185	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73170192	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7781827	0.80[CEU][hapmap]
rs7788316	0.80[CEU][hapmap]
rs7800196	0.89[CEU][hapmap]
rs7806429	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs883138	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs3735167	LRRC61	cis	Nerve Tibial	GTEx
rs3735167	LRRC61	cis	lymphoblastoid	seeQTL
rs3735167	LRRC61	cis	Adipose Subcutaneous	GTEx
rs3735167	ZBED6CL	cis	Whole Blood	GTEx
rs3735167	C7orf29	cis	multi-tissue	Pritchard
rs3735167	LRRC61	cis	parietal	SCAN
rs3735167	LRRC61	cis	Muscle Skeletal	GTEx
rs3735167	LRRC61	cis	Artery Tibial	GTEx
rs3735167	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs3735167	REPIN1	cis	Muscle Skeletal	GTEx
rs3735167	RARRES2	cis	multi-tissue	Pritchard
rs3735167	C7orf29	cis	lymphoblastoid	seeQTL
rs3735167	LRRC61	cis	Esophagus Mucosa	GTEx
rs3735167	C7orf29	cis	cerebellum	SCAN
rs3735167	LRRC61	cis	cerebellum	SCAN
rs3735167	ACTR3C	cis	Muscle Skeletal	GTEx
rs3735167	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs3735167	LRRC61	cis	lung	GTEx
rs3735167	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs3735167	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs3735167	LRRC61	cis	multi-tissue	Pritchard
rs3735167	LRRC61	cis	Thyroid	GTEx
rs3735167	RARRES2	cis	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150038600-150039600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
2	chr7:150038800-150039600	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr7:150038800-150040600	Enhancers	Liver	Liver
4	chr7:150038800-150052600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:150039000-150039600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
6	chr7:150039000-150039600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
7	chr7:150039000-150039600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
8	chr7:150039000-150039600	Flanking Bivalent TSS/Enh	HepG2	liver
9	chr7:150039200-150039600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr7:150039200-150039600	Enhancers	Pancreas	Pancrea
11	chr7:150039200-150039800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
12	chr7:150039200-150039800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:150039200-150040000	Bivalent Enhancer	K562	blood
14	chr7:150039200-150040200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:150039200-150040600	Weak transcription	Aorta	Aorta
16	chr7:150039200-150040600	Strong transcription	Dnd41	blood
17	chr7:150039200-150065000	Weak transcription	Right Atrium	heart
18	chr7:150039400-150039600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
19	chr7:150039400-150039600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:150039400-150039600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
21	chr7:150039400-150039600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
22	chr7:150039400-150039600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
23	chr7:150039400-150039600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:150039400-150039600	Bivalent Enhancer	Fetal Lung	lung
25	chr7:150039400-150039600	Enhancers	Ovary	ovary
26	chr7:150039400-150039600	Enhancers	Rectal Smooth Muscle	rectum
27	chr7:150039400-150039800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:150039400-150039800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr7:150039400-150039800	Bivalent Enhancer	Colonic Mucosa	Colon
30	chr7:150039400-150039800	Enhancers	Colon Smooth Muscle	Colon
31	chr7:150039400-150040600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:150039400-150040800	Enhancers	Fetal Intestine Small	intestine

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