Variant report

Variant	rs4687558
Chromosome Location	chr3:52890788-52890789
allele	C/T
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	GATA3	chr3:52890707-52891102	T-47D	breast:	n/a	chr3:52890857-52890867

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52888069..52891024-chr3:53081330..53083131,2	K562	blood:
2	chr3:52888488..52890920-chr3:53078565..53080433,2	MCF-7	breast:

Variant related genes	Relation type
TMEM110	TF binding region
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2336156	0.87[LWK][hapmap]
rs2564946	1.00[YRI][hapmap]
rs2710315	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2710317	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2710327	0.85[YRI][hapmap]
rs2710330	0.84[AFR][1000 genomes]
rs6776876	0.92[AFR][1000 genomes]
rs7629350	1.00[YRI][hapmap]

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	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
2	chr3:52873400-52891600	Strong transcription	Primary T cells from cord blood	blood
3	chr3:52873400-52892000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:52873800-52891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:52879800-52894800	Weak transcription	HSMM	muscle
6	chr3:52880600-52891000	Weak transcription	Fetal Heart	heart
7	chr3:52883400-52894200	Weak transcription	HSMMtube	muscle
8	chr3:52883400-52894600	Weak transcription	Hela-S3	cervix
9	chr3:52883800-52894400	Weak transcription	Psoas Muscle	Psoas
10	chr3:52884000-52898200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:52884200-52893000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:52884400-52893000	Weak transcription	Small Intestine	intestine
14	chr3:52885400-52899600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:52886000-52891000	Strong transcription	Fetal Thymus	thymus
16	chr3:52886200-52907800	Weak transcription	NHLF	lung
17	chr3:52886400-52894200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:52886600-52890800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:52886600-52890800	Weak transcription	Pancreas	Pancrea
20	chr3:52886600-52890800	Weak transcription	Right Ventricle	heart
21	chr3:52886600-52891000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:52886600-52891200	Weak transcription	Spleen	Spleen
23	chr3:52886600-52891400	Weak transcription	Brain Substantia Nigra	brain
24	chr3:52886600-52891600	Weak transcription	Fetal Lung	lung
25	chr3:52886600-52894400	Weak transcription	Esophagus	oesophagus
26	chr3:52886600-52894400	Weak transcription	Gastric	stomach
27	chr3:52886600-52894600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:52886600-52894600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:52886600-52895000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:52886600-52897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:52886600-52897600	Weak transcription	Fetal Intestine Small	intestine
32	chr3:52886600-52897800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:52886600-52898200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:52886600-52899800	Weak transcription	Dnd41	blood
35	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
39	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
41	chr3:52886800-52891800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:52886800-52893600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:52886800-52894400	Weak transcription	Placenta	Placenta
44	chr3:52886800-52894600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:52886800-52894800	Weak transcription	Brain Angular Gyrus	brain
46	chr3:52886800-52900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:52887000-52890800	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:52887000-52898000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:52887000-52898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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