Variant report

Variant	rs73878328
Chromosome Location	chr3:161132623-161132624
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160786404..160789728-chr3:161132273..161134989,3	MCF-7	breast:
2	chr3:160821447..160825392-chr3:161131716..161133453,3	MCF-7	breast:
3	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
4	chr17:77812966..77815600-chr3:161129810..161132642,2	MCF-7	breast:
5	chr3:161025355..161028351-chr3:161131512..161133073,2	MCF-7	breast:
6	chr3:160821926..160824694-chr3:161130720..161134424,3	MCF-7	breast:
7	chr3:160818689..160820412-chr3:161131602..161133156,2	MCF-7	breast:
8	chr12:64385805..64388155-chr3:161131123..161133119,2	MCF-7	breast:
9	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
10	chr3:160937705..160941241-chr3:161127569..161134417,11	MCF-7	breast:
11	chr3:161031194..161033997-chr3:161131950..161133763,3	MCF-7	breast:
12	chr3:161041936..161043684-chr3:161128783..161133001,3	MCF-7	breast:
13	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:
14	chr17:7387105..7389788-chr3:161131075..161133890,2	MCF-7	breast:
15	chr17:57922421..57925023-chr3:161131706..161133693,2	MCF-7	breast:
16	chr3:102426713..102428233-chr3:161131598..161134258,2	MCF-7	breast:
17	chr3:160818015..160820994-chr3:161127414..161132752,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271052	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000141582	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12632537	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12634006	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16832203	0.96[EUR][1000 genomes]
rs57175632	0.82[ASN][1000 genomes]
rs57278490	0.87[EUR][1000 genomes]
rs57496534	0.87[EUR][1000 genomes]
rs57803909	0.87[EUR][1000 genomes]
rs58350275	0.87[EUR][1000 genomes]
rs58557417	0.80[EUR][1000 genomes]
rs58562874	0.87[EUR][1000 genomes]
rs59541314	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59761692	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59964190	0.87[EUR][1000 genomes]
rs60172527	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs60400555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60612225	0.87[EUR][1000 genomes]
rs60684226	0.87[EUR][1000 genomes]
rs61048679	1.00[AMR][1000 genomes]
rs61217744	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73021435	0.82[ASN][1000 genomes]
rs73878307	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73878308	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73878311	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73878313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73878321	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73878322	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73878324	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73878325	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625217	0.87[EUR][1000 genomes]
rs873183	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs896080	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161124000-161133400	Weak transcription	Fetal Lung	lung
2	chr3:161125600-161137000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:161128000-161133200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:161128000-161133400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:161128200-161133200	Weak transcription	NHEK	skin
6	chr3:161128200-161133600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:161128200-161134000	Weak transcription	Esophagus	oesophagus
8	chr3:161129600-161133200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:161129600-161134600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:161130600-161134800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:161131400-161132800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:161131400-161133000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:161131400-161133800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:161131600-161132800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:161131600-161132800	Weak transcription	NHDF-Ad	bronchial
16	chr3:161131600-161133400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:161131600-161133400	Weak transcription	Brain Substantia Nigra	brain
18	chr3:161131600-161133600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:161131600-161133600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:161131600-161134000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:161131600-161134000	Weak transcription	Right Atrium	heart
22	chr3:161131600-161134200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:161131600-161140000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:161131800-161132800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:161131800-161132800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:161131800-161132800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:161131800-161132800	Weak transcription	Hela-S3	cervix
28	chr3:161131800-161132800	Weak transcription	Osteobl	bone
29	chr3:161131800-161133200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:161131800-161133200	Weak transcription	HMEC	breast
31	chr3:161131800-161133400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:161131800-161133400	Weak transcription	Brain Anterior Caudate	brain
33	chr3:161131800-161133400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:161131800-161133800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:161131800-161133800	Weak transcription	Fetal Muscle Leg	muscle
36	chr3:161131800-161134000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:161131800-161134000	Weak transcription	Aorta	Aorta
38	chr3:161131800-161134000	Weak transcription	Brain Angular Gyrus	brain
39	chr3:161131800-161134000	Weak transcription	Pancreas	Pancrea
40	chr3:161131800-161134000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:161131800-161134200	Weak transcription	Left Ventricle	heart
42	chr3:161131800-161134200	Weak transcription	NHLF	lung
43	chr3:161132000-161133600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:161132400-161134000	Enhancers	NH-A	brain
45	chr3:161132400-161134400	Enhancers	Adipose Nuclei	Adipose
46	chr3:161132400-161134600	Enhancers	Stomach Mucosa	stomach
47	chr3:161132600-161133400	Enhancers	HUVEC	blood vessel

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