Variant report

Variant	rs59960641
Chromosome Location	chr3:139065429-139065430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:139065369-139065563	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139061660..139066893-chr3:139105523..139110764,11	K562	blood:
2	chr3:139063205..139066777-chr3:139105523..139110764,7	K562	blood:

Variant related genes	Relation type
MRPS22	TF binding region
ENSG00000248932	Chromatin interaction
ENSG00000252245	Chromatin interaction
ENSG00000184432	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10513063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1602626	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1602628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17316181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17335312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17394620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17395611	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17494356	0.85[ASN][1000 genomes]
rs17560106	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1844977	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289348	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2289350	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2291555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2307031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772876	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs41356949	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs41399544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55922868	0.90[ASN][1000 genomes]
rs56993164	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57356584	0.89[EUR][1000 genomes]
rs57995350	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58060926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59628512	0.90[ASN][1000 genomes]
rs59958973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61034702	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61613889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61680644	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005158	chr3:139001736-139073011	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	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
3	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139063600-139066000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:139063800-139070000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:139064000-139065600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:139064000-139065800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:139064000-139065800	Weak transcription	Colonic Mucosa	Colon
6	chr3:139064000-139065800	Weak transcription	Right Ventricle	heart
7	chr3:139064000-139066000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:139064000-139066000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:139064000-139066000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:139064000-139066000	Weak transcription	Esophagus	oesophagus
11	chr3:139064000-139066000	Weak transcription	Left Ventricle	heart
12	chr3:139064000-139066000	Weak transcription	Lung	lung
13	chr3:139064000-139066400	Weak transcription	Placenta	Placenta
14	chr3:139064000-139067000	Weak transcription	Fetal Kidney	kidney
15	chr3:139064000-139070200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:139064000-139073400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:139064000-139073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:139064000-139073600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:139064200-139065600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:139064200-139065600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:139064200-139065600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:139064200-139065600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:139064200-139065600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:139064200-139065600	Weak transcription	Fetal Stomach	stomach
25	chr3:139064200-139065800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:139064200-139065800	Weak transcription	HSMMtube	muscle
27	chr3:139064200-139066000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:139064200-139066000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:139064200-139066000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:139064200-139066000	Weak transcription	Spleen	Spleen
31	chr3:139064200-139066600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:139064200-139067200	Weak transcription	NHLF	lung
33	chr3:139064200-139068200	Weak transcription	Stomach Mucosa	stomach
34	chr3:139064200-139068200	Weak transcription	A549	lung
35	chr3:139064200-139072600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:139064200-139089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:139064400-139065800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:139064400-139065800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:139064400-139066000	Weak transcription	Fetal Intestine Small	intestine
40	chr3:139064400-139097200	Strong transcription	Fetal Muscle Leg	muscle
41	chr3:139064600-139065600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:139064600-139065600	Weak transcription	Fetal Lung	lung
43	chr3:139064600-139065800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:139064600-139065800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:139064600-139065800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:139064600-139065800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:139064600-139066000	Weak transcription	Thymus	Thymus
48	chr3:139064600-139066400	Weak transcription	Fetal Brain Male	brain
49	chr3:139064600-139067000	Weak transcription	Ovary	ovary
50	chr3:139064600-139069600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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