Variant report

Variant	rs11714087
Chromosome Location	chr3:142405348-142405349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142400757..142403430-chr3:142404368..142406089,2	K562	blood:
2	chr17:41399646..41402633-chr3:142404029..142407052,5	K562	blood:
3	chr17:41380707..41383716-chr3:142404049..142407051,3	MCF-7	breast:
4	chr17:41464662..41468162-chr3:142404033..142407052,7	K562	blood:
5	chr17:41464575..41468162-chr3:142404053..142407052,8	K562	blood:

Variant related genes	Relation type
ENSG00000188825	Chromatin interaction
ENSG00000236383	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11709121	1.00[CEU][hapmap];0.86[GIH][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs11711434	0.84[AMR][1000 genomes]
rs1403726	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17623058	0.84[AMR][1000 genomes]
rs2049329	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2140435	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2140436	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272150	0.85[EUR][1000 genomes]
rs55951550	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56161530	0.84[AMR][1000 genomes]
rs56328361	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440100	0.95[EUR][1000 genomes]
rs73230564	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11714087	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:32 , 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	chr3:142379200-142413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:142384400-142411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:142385800-142415400	Weak transcription	A549	lung
6	chr3:142386400-142411800	Weak transcription	NHEK	skin
7	chr3:142387400-142413400	Weak transcription	Stomach Mucosa	stomach
8	chr3:142389200-142412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:142389200-142414800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:142389400-142408800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:142389400-142410000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:142390000-142406200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:142392600-142410200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:142392800-142418000	Weak transcription	HepG2	liver
16	chr3:142392800-142425400	Weak transcription	Dnd41	blood
17	chr3:142392800-142433000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:142393000-142407000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:142393000-142426000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:142393400-142426200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:142399400-142407200	Weak transcription	Esophagus	oesophagus
22	chr3:142400200-142406200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr3:142401200-142410000	Weak transcription	Primary T cells from cord blood	blood
24	chr3:142402400-142408800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr3:142403000-142406000	Strong transcription	Liver	Liver
26	chr3:142403000-142412800	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr3:142403600-142406400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:142404200-142405800	Strong transcription	Fetal Intestine Large	intestine
29	chr3:142404200-142418000	Weak transcription	HMEC	breast
30	chr3:142404600-142405400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:142404600-142406800	Weak transcription	Fetal Thymus	thymus
32	chr3:142404600-142416200	Weak transcription	Fetal Intestine Small	intestine

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