Variant report

Variant	rs6789881
Chromosome Location	chr3:119040523-119040524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr3:119040440-119040653	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:119040475-119042774	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:119040439-119040870	GM12892	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119040381..119043387-chr3:119393976..119396207,3	K562	blood:
2	chr3:119039655..119042714-chr3:119058706..119061390,3	MCF-7	breast:
3	chr3:119016211..119028042-chr3:119037960..119043695,12	MCF-7	breast:
4	chr3:119012312..119014941-chr3:119040203..119043471,4	MCF-7	breast:
5	chr3:119040520..119043561-chr3:119060040..119062334,3	MCF-7	breast:

No data

Variant related genes	Relation type
ARHGAP31	TF binding region
ENSG00000242829	Chromatin interaction
ENSG00000138495	Chromatin interaction
ENSG00000207310	Chromatin interaction
ENSG00000031081	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10511386	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10934490	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497738	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314464	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375135	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448434	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2278781	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4687994	0.83[EUR][1000 genomes]
rs58568360	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62265236	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62265237	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438518	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438519	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438520	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6438521	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6438522	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438523	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6762580	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6785727	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786522	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799733	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610546	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7611832	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7619210	0.82[EUR][1000 genomes]
rs7644570	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7649480	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7649930	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822211	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825078	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9834750	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847963	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9861372	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861688	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877740	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119015000-119041200	Weak transcription	Aorta	Aorta
2	chr3:119015200-119041000	Weak transcription	Fetal Kidney	kidney
3	chr3:119016000-119041000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:119016400-119040800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:119016400-119041000	Weak transcription	Fetal Intestine Small	intestine
6	chr3:119017400-119040600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:119019200-119040800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:119020400-119040600	Weak transcription	Esophagus	oesophagus
9	chr3:119021200-119041000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:119021200-119041000	Weak transcription	Fetal Thymus	thymus
11	chr3:119022200-119040800	Weak transcription	Brain Angular Gyrus	brain
12	chr3:119022400-119040600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:119022400-119041000	Weak transcription	Primary B cells from cord blood	blood
14	chr3:119022400-119041000	Weak transcription	Fetal Intestine Large	intestine
15	chr3:119022400-119041200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:119022600-119040600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:119024400-119040600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:119024800-119040600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:119024800-119041000	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:119024800-119041000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:119025000-119040800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:119027600-119041000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:119029600-119041200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:119030000-119041000	Weak transcription	Brain Anterior Caudate	brain
25	chr3:119030000-119041200	Weak transcription	Gastric	stomach
26	chr3:119030200-119041000	Weak transcription	Colonic Mucosa	Colon
27	chr3:119030800-119040800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:119031000-119040600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:119031000-119040600	Weak transcription	NHDF-Ad	bronchial
30	chr3:119031000-119041000	Weak transcription	NHLF	lung
31	chr3:119031200-119040600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:119031200-119041000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:119031200-119041200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:119031400-119041000	Weak transcription	NHEK	skin
35	chr3:119033200-119040600	Weak transcription	Pancreas	Pancrea
36	chr3:119033200-119041000	Weak transcription	Thymus	Thymus
37	chr3:119033400-119040600	Weak transcription	Osteobl	bone
38	chr3:119033400-119041000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:119033400-119041200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:119033600-119040600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:119033600-119040600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:119033600-119040600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:119033600-119040800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:119033600-119041000	Weak transcription	Primary T cells from cord blood	blood
45	chr3:119033800-119040800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr3:119034000-119040600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:119034400-119041000	Weak transcription	Brain Substantia Nigra	brain
48	chr3:119034600-119040600	Weak transcription	Lung	lung
49	chr3:119034600-119041000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:119034600-119041000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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