Variant report

Variant	rs2306201
Chromosome Location	chr19:38077474-38077475
allele	C/T
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:1)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38076622..38080625-chr19:38081977..38086090,6	MCF-7	breast:

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF793-1	chr19:38076240-38078249	ENSG00000267470.1
2	lnc-ZNF793-1	chr19:38076240-38078248	NONHSAT066134
3	lnc-ZNF793-1	chr19:38076240-38078248	NONHSAT066138
4	lnc-ZNF793-1	chr19:38076240-38078249	ENSG00000267470.1
5	lnc-ZNF793-1	chr19:38076240-38078248	NR_038247
6	lnc-ZNF793-1	chr19:38076240-38078248	NR_038249
7	lnc-ZNF793-1	chr19:38076240-38078249	ENSG00000267470.1

No data

Variant related genes	Relation type
ENSG00000171817	Chromatin interaction
ENSG00000180479	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10419281	0.82[ASW][hapmap]
rs10445548	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048505	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061756	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244713	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17303902	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304703	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305193	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305228	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305823	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306900	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs1871196	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385005	0.96[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2385180	1.00[ASW][hapmap]
rs35153242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681348	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55718806	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55743020	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865869	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909413	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277404	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56351266	0.86[ASN][1000 genomes]
rs57654288	0.99[EUR][1000 genomes]
rs57943942	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62108291	0.83[EUR][1000 genomes]
rs62108306	0.82[EUR][1000 genomes]
rs7245855	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs7254009	0.82[ASW][hapmap]
rs7259272	0.92[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs73031330	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033122	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033134	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033142	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035159	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73035160	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039029	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[ASN][1000 genomes]
rs8101610	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104282	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108268	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109103	1.00[ASW][hapmap]
rs8111790	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs2306201	AC012309.5	cis	Thyroid	GTEx
rs2306201	AC012309.5	cis	Muscle Skeletal	GTEx
rs2306201	AC012309.5	cis	Esophagus Muscularis	GTEx
rs2306201	C19orf61	cis	cerebellum	SCAN
rs2306201	PAK4	cis	cerebellum	SCAN
rs2306201	PHLDB3	cis	cerebellum	SCAN
rs2306201	DMPK	cis	parietal	SCAN
rs2306201	PVR	cis	parietal	SCAN
rs2306201	RASGRP4	cis	parietal	SCAN
rs2306201	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2306201	AC012309.5	cis	Heart Left Ventricle	GTEx
rs2306201	PLEKHG2	cis	cerebellum	SCAN
rs2306201	AC012309.5	cis	Esophagus Mucosa	GTEx
rs2306201	CEACAM3	cis	parietal	SCAN
rs2306201	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs2306201	AC012309.5	cis	lung	GTEx
rs2306201	ZNF781	cis	Thyroid	GTEx
rs2306201	AC012309.5	cis	Artery Tibial	GTEx
rs2306201	POU2F2	cis	parietal	SCAN
rs2306201	ZNF781	trans	cerebellum	SCAN
rs2306201	CCDC97	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38032400-38080800	ZNF genes & repeats	Liver	Liver
2	chr19:38038000-38078400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38038600-38079600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:38041200-38079600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:38045000-38078600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:38046600-38079600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
7	chr19:38047400-38078600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
8	chr19:38049200-38079600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:38051600-38077600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
10	chr19:38051600-38078800	ZNF genes & repeats	Fetal Brain Female	brain
11	chr19:38052200-38078600	ZNF genes & repeats	Primary B cells from cord blood	blood
12	chr19:38053200-38078200	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr19:38053200-38078600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:38053400-38078400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
15	chr19:38059800-38078000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr19:38065200-38078800	ZNF genes & repeats	Colon Smooth Muscle	Colon
17	chr19:38065800-38078400	ZNF genes & repeats	Primary T cells from cord blood	blood
18	chr19:38065800-38078600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr19:38068200-38078200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
20	chr19:38068400-38078000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
21	chr19:38068400-38078200	ZNF genes & repeats	Fetal Muscle Leg	muscle
22	chr19:38068400-38078400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:38068400-38078600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:38068400-38078800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr19:38068600-38077600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
26	chr19:38068600-38078200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
27	chr19:38068600-38078400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:38068600-38080000	ZNF genes & repeats	Ovary	ovary
29	chr19:38068600-38080800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr19:38068800-38078200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
31	chr19:38068800-38079800	ZNF genes & repeats	Dnd41	blood
32	chr19:38069200-38079600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
33	chr19:38069600-38077800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
34	chr19:38069800-38084600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:38070400-38077800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:38070400-38079600	ZNF genes & repeats	Fetal Lung	lung
37	chr19:38070600-38079600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:38071000-38078800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:38071200-38078800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
40	chr19:38071200-38079600	ZNF genes & repeats	Fetal Kidney	kidney
41	chr19:38071400-38078600	ZNF genes & repeats	Aorta	Aorta
42	chr19:38072400-38077800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:38072400-38078800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
44	chr19:38072400-38084600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr19:38072800-38077600	Strong transcription	Placenta	Placenta
46	chr19:38072800-38078600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
47	chr19:38073000-38077600	ZNF genes & repeats	Fetal Intestine Large	intestine
48	chr19:38073000-38078200	ZNF genes & repeats	Left Ventricle	heart
49	chr19:38073200-38078000	ZNF genes & repeats	Lung	lung
50	chr19:38073200-38079600	ZNF genes & repeats	Brain Substantia Nigra	brain

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