Variant report

Variant	rs3800781
Chromosome Location	chr7:150027324-150027325
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150027152..150029852-chr7:150062347..150064947,2	K562	blood:
2	chr7:150027322..150029064-chr7:150097109..150099417,2	K562	blood:
3	chr7:150019910..150022890-chr7:150026315..150029098,3	MCF-7	breast:
4	chr7:150026896..150029786-chr7:150064895..150066842,2	MCF-7	breast:
5	chr7:150025749..150027399-chr7:150065902..150067517,2	MCF-7	breast:

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

Extended variants
information (count: 86 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10282458	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1047207	0.92[EUR][1000 genomes]
rs1047575	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1047586	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10952249	0.85[EUR][1000 genomes]
rs10952250	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10952252	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11764936	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11765644	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11765692	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11766288	0.90[EUR][1000 genomes]
rs11767726	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11769348	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773351	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11974980	0.85[EUR][1000 genomes]
rs11975886	0.85[EUR][1000 genomes]
rs11983355	0.88[EUR][1000 genomes]
rs1464752	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1464753	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17173617	0.92[EUR][1000 genomes]
rs17837498	0.85[EUR][1000 genomes]
rs1916932	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1962004	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1983440	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2098053	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2108851	0.88[EUR][1000 genomes]
rs2108852	0.88[EUR][1000 genomes]
rs2108853	0.88[EUR][1000 genomes]
rs2108854	0.88[EUR][1000 genomes]
rs2159234	0.88[EUR][1000 genomes]
rs2159235	0.88[EUR][1000 genomes]
rs2159236	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2373751	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28432021	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28439010	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3088207	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34489187	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3735167	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3735169	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3735170	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3735171	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3735172	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3735173	0.90[EUR][1000 genomes]
rs3735174	0.90[EUR][1000 genomes]
rs3735175	0.88[EUR][1000 genomes]
rs3800780	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4395803	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4554381	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55715989	0.85[EUR][1000 genomes]
rs55881542	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55974958	0.92[EUR][1000 genomes]
rs56019796	0.85[EUR][1000 genomes]
rs56190213	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56402329	0.82[EUR][1000 genomes]
rs56923535	0.85[EUR][1000 genomes]
rs56998970	0.86[EUR][1000 genomes]
rs57888387	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59572505	0.85[EUR][1000 genomes]
rs60268791	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60283368	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60467296	0.85[EUR][1000 genomes]
rs61421252	0.92[EUR][1000 genomes]
rs6964110	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73170169	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73170174	0.88[EUR][1000 genomes]
rs73170185	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73170192	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7781827	0.85[EUR][1000 genomes]
rs7788316	0.85[EUR][1000 genomes]
rs7806429	0.85[EUR][1000 genomes]
rs883138	0.88[EUR][1000 genomes];0.85[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	nsv516052	chr7:150020295-150034184	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv518774	chr7:150020295-150036664	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs3800781	LRRC61	cis	Artery Tibial	GTEx
rs3800781	ZBED6CL	cis	Esophagus Mucosa	GTEx
rs3800781	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs3800781	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs3800781	LRRC61	cis	Artery Aorta	GTEx
rs3800781	ACTR3C	cis	Muscle Skeletal	GTEx
rs3800781	LRRC61	cis	Whole Blood	GTEx
rs3800781	LRRC61	cis	Thyroid	GTEx
rs3800781	LRRC61	cis	Muscle Skeletal	GTEx
rs3800781	REPIN1	cis	Muscle Skeletal	GTEx
rs3800781	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs3800781	ZBED6CL	cis	Whole Blood	GTEx
rs3800781	ZBED6CL	cis	Stomach	GTEx
rs3800781	LRRC61	cis	Adipose Subcutaneous	GTEx
rs3800781	LRRC61	cis	Esophagus Mucosa	GTEx
rs3800781	LRRC61	cis	lung	GTEx
rs3800781	RARRES2	cis	multi-tissue	Pritchard
rs3800781	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs3800781	LRRC61	cis	Nerve Tibial	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150020400-150030000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:150021400-150029400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:150021400-150037000	Weak transcription	Brain Substantia Nigra	brain
4	chr7:150021600-150028800	Weak transcription	NHEK	skin
5	chr7:150021800-150030800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:150021800-150032600	Weak transcription	Brain Angular Gyrus	brain
7	chr7:150021800-150033600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:150021800-150037200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:150022000-150032200	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:150022000-150032200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:150022000-150036400	Weak transcription	Fetal Kidney	kidney
12	chr7:150022200-150031400	Strong transcription	Thymus	Thymus
13	chr7:150022200-150031600	Strong transcription	Fetal Stomach	stomach
14	chr7:150022200-150037200	Weak transcription	Small Intestine	intestine
15	chr7:150022400-150027400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:150022400-150029200	Weak transcription	Right Atrium	heart
17	chr7:150022400-150031200	Strong transcription	Primary T cells from cord blood	blood
18	chr7:150022400-150032200	Strong transcription	Fetal Intestine Small	intestine
19	chr7:150022400-150035600	Weak transcription	Fetal Heart	heart
20	chr7:150022400-150037400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:150022600-150028200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:150022600-150029000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:150022600-150029200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:150022600-150029400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr7:150022600-150029600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:150022600-150030000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:150022600-150031000	Strong transcription	Fetal Intestine Large	intestine
28	chr7:150022600-150031200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:150022600-150031400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr7:150022600-150031400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:150022600-150031400	Strong transcription	Fetal Thymus	thymus
32	chr7:150022600-150036800	Strong transcription	Fetal Brain Female	brain
33	chr7:150022800-150027600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr7:150022800-150028800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:150022800-150029000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr7:150022800-150030800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:150022800-150033800	Weak transcription	Right Ventricle	heart
38	chr7:150023000-150027800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr7:150023000-150028400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr7:150023000-150028600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr7:150023000-150028800	Strong transcription	Lung	lung
42	chr7:150023000-150030200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:150023000-150030800	Strong transcription	Liver	Liver
44	chr7:150023000-150032400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:150023200-150029000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr7:150023600-150030000	Strong transcription	Placenta	Placenta
47	chr7:150023800-150028400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr7:150023800-150028400	Strong transcription	Rectal Smooth Muscle	rectum
49	chr7:150024000-150030200	Strong transcription	HepG2	liver
50	chr7:150024000-150031400	Strong transcription	Hela-S3	cervix

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