Variant report

Variant	rs1980190
Chromosome Location	chr3:141457998-141457999
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141455674..141460093-chr3:141592801..141597430,19	MCF-7	breast:
2	chr3:141452499..141459593-chr3:141591792..141599045,17	MCF-7	breast:
3	chr3:141457377..141459578-chr3:141597906..141599752,2	MCF-7	breast:
4	chr3:141456676..141459122-chr3:141866884..141869547,2	MCF-7	breast:
5	chr3:141455466..141460652-chr3:141593125..141598625,15	K562	blood:
6	chr3:141378869..141381397-chr3:141457213..141459259,2	MCF-7	breast:
7	chr3:141457369..141459692-chr3:141539013..141541965,2	MCF-7	breast:
8	chr3:141455463..141459614-chr3:141593520..141599146,20	K562	blood:
9	chr3:141455584..141459326-chr3:141464266..141467931,6	MCF-7	breast:
10	chr3:141448745..141449381-chr3:141457616..141458482,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction
ENSG00000114125	Chromatin interaction
ENSG00000114126	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1055690	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs61270966	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440034	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6776205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73000305	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7635763	0.92[CHB][hapmap]
rs9789997	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877552	chr3:141420562-141466147	Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1980190	GRK7	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141456400-141458200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:141456600-141458000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:141456600-141458000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:141456600-141458000	Active TSS	Fetal Heart	heart
5	chr3:141456600-141458200	Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr3:141456600-141458200	Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr3:141456600-141458200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr3:141456600-141458200	Active TSS	Brain Cingulate Gyrus	brain
9	chr3:141456600-141458200	Active TSS	Colon Smooth Muscle	Colon
10	chr3:141456600-141458200	Active TSS	Left Ventricle	heart
11	chr3:141456600-141458200	Active TSS	Placenta Amnion	Placenta Amnion
12	chr3:141456600-141458200	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr3:141456600-141458200	Active TSS	Stomach Mucosa	stomach
14	chr3:141456600-141458200	Active TSS	Hela-S3	cervix
15	chr3:141456600-141458200	Active TSS	Osteobl	bone
16	chr3:141456600-141458400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr3:141456600-141458400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr3:141456600-141458400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr3:141456600-141458400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:141456600-141458400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:141456600-141458400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr3:141456600-141458400	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr3:141456600-141458400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:141456600-141458400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:141456600-141458400	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr3:141456600-141458400	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr3:141456600-141458400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:141456600-141458400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:141456600-141458400	Active TSS	Brain Anterior Caudate	brain
30	chr3:141456600-141458400	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr3:141456600-141458400	Active TSS	Brain Substantia Nigra	brain
32	chr3:141456600-141458400	Active TSS	Duodenum Mucosa	Duodenum
33	chr3:141456600-141458400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr3:141456600-141458400	Active TSS	Fetal Lung	lung
35	chr3:141456600-141458400	Active TSS	Fetal Stomach	stomach
36	chr3:141456600-141458400	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr3:141456600-141458400	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr3:141456600-141458400	Active TSS	A549	lung
39	chr3:141456600-141458400	Active TSS	HMEC	breast
40	chr3:141456600-141458400	Active TSS	HUVEC	blood vessel
41	chr3:141456600-141458400	Active TSS	NHEK	skin
42	chr3:141456600-141458600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:141456600-141458600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:141456600-141458600	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr3:141456600-141458600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:141456600-141458600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:141456600-141458600	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr3:141456600-141458600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:141456600-141458600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:141456600-141458600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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