Variant report

Variant	rs34846983
Chromosome Location	chr19:39625326-39625327
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39624966..39625536-chr19:39678054..39678776,2	MCF-7	breast:
2	chr19:39619372..39620875-chr19:39624285..39626260,2	K562	blood:
3	chr19:39624151..39625876-chr19:39627199..39629585,2	K562	blood:
4	chr19:39618750..39620262-chr19:39623192..39625353,2	K562	blood:
5	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:
6	chr19:39624644..39625575-chr19:39641363..39642260,6	MCF-7	breast:
7	chr19:39622591..39626006-chr19:39627126..39631368,3	MCF-7	breast:
8	chr19:39624651..39625632-chr19:39641254..39641826,3	MCF-7	breast:
9	chr19:39624660..39625575-chr19:39641363..39642260,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1077457	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1079442	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083509	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083510	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12610624	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12611361	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12611365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12611376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12984418	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17722300	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17795295	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2082417	0.83[ASN][1000 genomes]
rs2873913	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34058542	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34110379	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34270590	0.81[EUR][1000 genomes]
rs34326918	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34808880	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35163943	0.81[EUR][1000 genomes]
rs35591784	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36148214	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3889485	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55748546	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61171111	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67248178	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71356838	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71356839	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71356840	0.83[EUR][1000 genomes]
rs71356841	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs737450	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8107629	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	esv2545161	chr19:39624402-39625800	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2008944	chr19:39624915-39625584	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617000-39630800	Weak transcription	Primary T cells from cord blood	blood
2	chr19:39617000-39635000	Weak transcription	Aorta	Aorta
3	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:39617600-39625600	Enhancers	Spleen	Spleen
5	chr19:39617600-39627600	Enhancers	Fetal Heart	heart
6	chr19:39617800-39627200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr19:39617800-39628600	Enhancers	Placenta	Placenta
8	chr19:39617800-39630200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
10	chr19:39618200-39628400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr19:39618400-39626800	Weak transcription	NHEK	skin
12	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr19:39620000-39627200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:39620000-39630000	Weak transcription	HepG2	liver
15	chr19:39620600-39626800	Enhancers	Fetal Intestine Large	intestine
16	chr19:39621000-39627200	Enhancers	Fetal Lung	lung
17	chr19:39621000-39628400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:39621400-39628000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr19:39621600-39627800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr19:39621800-39627400	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr19:39622200-39627200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:39622200-39628200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr19:39622400-39627000	Weak transcription	Small Intestine	intestine
24	chr19:39622400-39629000	Weak transcription	NH-A	brain
25	chr19:39622400-39635200	Weak transcription	Fetal Brain Female	brain
26	chr19:39622600-39639600	Weak transcription	HSMM	muscle
27	chr19:39622800-39626800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:39622800-39627400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:39623000-39635200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr19:39623400-39626800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:39623400-39629000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:39623600-39625600	Enhancers	Fetal Intestine Small	intestine
34	chr19:39623600-39626800	Weak transcription	Adipose Nuclei	Adipose
35	chr19:39623600-39627200	Weak transcription	HUVEC	blood vessel
36	chr19:39623600-39630200	Weak transcription	Brain Angular Gyrus	brain
37	chr19:39623800-39627400	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:39623800-39630200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:39624000-39647000	Weak transcription	NHLF	lung
40	chr19:39624200-39629000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr19:39624200-39630200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr19:39624200-39634800	Weak transcription	Fetal Kidney	kidney
43	chr19:39624400-39625800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:39624400-39626400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:39624400-39626400	Weak transcription	A549	lung
46	chr19:39624400-39626800	Weak transcription	Brain Substantia Nigra	brain
47	chr19:39624400-39627000	Weak transcription	HMEC	breast
48	chr19:39624400-39627400	Weak transcription	Brain Germinal Matrix	brain
49	chr19:39624400-39628200	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr19:39624400-39628600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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