Variant report

Variant	rs2140436
Chromosome Location	chr3:142389669-142389670
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142387225..142389939-chr3:142390380..142394474,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199319	Chromatin interaction

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

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

rs_ID	r²[population]
rs11709121	0.86[EUR][1000 genomes]
rs11711434	0.81[EUR][1000 genomes]
rs11714087	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11717988	0.82[AMR][1000 genomes]
rs1403726	0.86[CHB][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17623058	0.81[EUR][1000 genomes]
rs2049329	0.95[EUR][1000 genomes]
rs2140435	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272150	0.89[EUR][1000 genomes]
rs55655603	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs55851231	0.82[AMR][1000 genomes]
rs55951550	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56161530	0.81[EUR][1000 genomes]
rs56239979	0.82[AMR][1000 genomes]
rs56246347	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs56328361	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56397702	1.00[AFR][1000 genomes]
rs6440100	0.95[EUR][1000 genomes]
rs73228762	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs73228782	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73228788	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73230564	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73230583	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73230587	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73230588	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73230590	0.82[AMR][1000 genomes]
rs73232704	0.82[AMR][1000 genomes]
rs73232707	0.82[AMR][1000 genomes]
rs73232714	0.82[AMR][1000 genomes]
rs73232716	0.82[AMR][1000 genomes]
rs9683274	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142369400-142408400	Weak transcription	Pancreas	Pancrea
3	chr3:142371000-142393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:142372600-142391200	Weak transcription	K562	blood
5	chr3:142379200-142413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:142380000-142390000	Weak transcription	Dnd41	blood
7	chr3:142380000-142390400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:142380000-142391800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:142380200-142391000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:142382600-142400400	Weak transcription	Gastric	stomach
11	chr3:142384400-142411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:142384600-142392400	Weak transcription	HepG2	liver
13	chr3:142384800-142390400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:142384800-142403000	Weak transcription	Liver	Liver
15	chr3:142385200-142391800	Weak transcription	Fetal Intestine Large	intestine
16	chr3:142385800-142391200	Weak transcription	Fetal Intestine Small	intestine
17	chr3:142385800-142415400	Weak transcription	A549	lung
18	chr3:142386400-142411800	Weak transcription	NHEK	skin
19	chr3:142387400-142401800	Weak transcription	Aorta	Aorta
20	chr3:142387400-142404200	Weak transcription	Small Intestine	intestine
21	chr3:142387400-142413400	Weak transcription	Stomach Mucosa	stomach
22	chr3:142388200-142393200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr3:142388200-142393200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr3:142388800-142389800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:142388800-142390000	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:142388800-142390800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr3:142389000-142389800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:142389200-142392000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:142389200-142412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:142389200-142414800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:142389400-142390200	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr3:142389400-142391600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:142389400-142408800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:142389400-142410000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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