Variant report

Variant	rs61680644
Chromosome Location	chr3:139174571-139174572
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139174418..139175114-chr3:139280608..139281156,2	MCF-7	breast:
2	chr3:139168645..139171256-chr3:139173067..139176313,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10513063	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1602626	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1602628	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17316181	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17335312	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17394620	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17395611	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17494356	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17494482	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17560106	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2233818	0.81[AFR][1000 genomes]
rs2289348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289350	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291555	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2307031	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2882080	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2882081	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3772871	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3772876	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41356949	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41399544	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55922868	0.90[ASN][1000 genomes]
rs56993164	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57707457	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57995350	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58060926	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59628512	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59958973	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59960641	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61034702	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61613889	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7428398	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9821204	0.85[ASN][1000 genomes]
rs9837167	0.85[ASN][1000 genomes]
rs9862672	0.85[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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1000519	chr3:139159300-139206245	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2752377	chr3:139163302-139188302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
2	chr3:139154200-139178600	Weak transcription	Left Ventricle	heart
3	chr3:139158600-139174800	Weak transcription	Adipose Nuclei	Adipose
4	chr3:139160200-139174800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:139160600-139174800	Weak transcription	Fetal Brain Male	brain
6	chr3:139163400-139189000	Weak transcription	Small Intestine	intestine
7	chr3:139163800-139180200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:139165800-139178600	Weak transcription	Right Ventricle	heart
9	chr3:139166000-139179000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:139167000-139175400	Weak transcription	Fetal Brain Female	brain
11	chr3:139167400-139174800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:139167400-139176000	Weak transcription	Brain Anterior Caudate	brain
13	chr3:139168000-139175200	Weak transcription	Brain Angular Gyrus	brain
14	chr3:139168600-139196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:139169200-139175000	Genic enhancers	Fetal Intestine Small	intestine
16	chr3:139170800-139174600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:139171200-139210200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:139171400-139174800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:139171400-139175800	Weak transcription	Brain Substantia Nigra	brain
20	chr3:139171400-139179400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr3:139171400-139179400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:139171800-139176000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr3:139171800-139176200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:139172000-139175600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:139172000-139176200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr3:139172000-139176200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:139172200-139175400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:139172400-139175400	Enhancers	H9 Cell Line	embryonic stem cell
29	chr3:139172400-139177000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:139172600-139175200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr3:139173200-139174800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr3:139173400-139175000	Enhancers	Brain Germinal Matrix	brain
33	chr3:139173400-139175600	Genic enhancers	Fetal Intestine Large	intestine
34	chr3:139173800-139175400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:139173800-139178400	Weak transcription	Fetal Muscle Leg	muscle
36	chr3:139173800-139180600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:139173800-139180600	Weak transcription	Pancreas	Pancrea
38	chr3:139174000-139174600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:139174200-139176800	Enhancers	Ovary	ovary
40	chr3:139174400-139174800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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