Variant report

Variant	rs12124
Chromosome Location	chr2:86253508-86253509
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86114460..86116872-chr2:86251867..86254759,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232504	Chromatin interaction
ENSG00000115525	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10168997	0.81[ASN][1000 genomes]
rs10184159	0.89[ASN][1000 genomes]
rs11689889	0.86[CHB][hapmap]
rs12328643	1.00[MEX][hapmap]
rs12329034	1.00[MEX][hapmap]
rs13403950	1.00[AMR][1000 genomes]
rs1469981	0.83[ASN][1000 genomes]
rs17026904	0.89[ASN][1000 genomes]
rs17026975	1.00[MEX][hapmap]
rs17579744	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1978842	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2241434	1.00[GIH][hapmap]
rs2278532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2278533	0.89[ASN][1000 genomes]
rs2278534	0.89[ASN][1000 genomes]
rs2278535	0.89[ASN][1000 genomes]
rs2278537	0.93[ASN][1000 genomes]
rs2288116	0.89[ASN][1000 genomes]
rs35239368	1.00[AMR][1000 genomes]
rs3731822	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3755005	0.93[ASN][1000 genomes]
rs3770063	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3770064	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs3770076	0.89[ASN][1000 genomes]
rs3770083	0.89[ASN][1000 genomes]
rs3770084	0.89[ASN][1000 genomes]
rs3770085	0.89[ASN][1000 genomes]
rs3770086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3770088	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3770091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3821019	0.89[ASN][1000 genomes]
rs56861544	0.91[ASN][1000 genomes]
rs57150140	0.89[ASN][1000 genomes]
rs57318396	0.91[ASN][1000 genomes]
rs57361751	1.00[ASN][1000 genomes]
rs57405155	1.00[ASN][1000 genomes]
rs57963460	0.91[ASN][1000 genomes]
rs58009603	0.89[ASN][1000 genomes]
rs58026145	0.89[ASN][1000 genomes]
rs58429119	0.80[ASN][1000 genomes]
rs58861315	0.89[ASN][1000 genomes]
rs58913632	1.00[ASN][1000 genomes]
rs58919291	0.89[ASN][1000 genomes]
rs59053280	0.89[ASN][1000 genomes]
rs60329449	0.86[ASN][1000 genomes]
rs60336356	0.93[ASN][1000 genomes]
rs60471596	0.80[ASN][1000 genomes]
rs61056382	0.93[ASN][1000 genomes]
rs61094144	0.93[ASN][1000 genomes]
rs61185790	0.89[ASN][1000 genomes]
rs61199255	0.91[ASN][1000 genomes]
rs61254540	0.89[ASN][1000 genomes]
rs6708805	0.83[ASN][1000 genomes]
rs6741224	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6755228	0.89[ASN][1000 genomes]
rs6760112	0.80[ASN][1000 genomes]
rs72847838	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12124	LOC90784	cis	lymphoblastoid	seeQTL
rs12124	ENSG00000068654	cis	multi-tissue	Pritchard
rs12124	POLR1A	cis	multi-tissue	Pritchard
rs12124	POLR1A	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86244200-86257000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:86244400-86255000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:86244600-86255200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:86244600-86257200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:86244800-86253600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:86245400-86254000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:86245400-86254600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:86245400-86257200	Weak transcription	Stomach Mucosa	stomach
9	chr2:86245400-86257400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:86245400-86263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:86245600-86253600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:86248400-86254200	Weak transcription	NHDF-Ad	bronchial
13	chr2:86248800-86257000	Weak transcription	Psoas Muscle	Psoas
14	chr2:86248800-86257200	Weak transcription	Fetal Kidney	kidney
15	chr2:86249000-86254200	Weak transcription	HUVEC	blood vessel
16	chr2:86249000-86255200	Weak transcription	Right Atrium	heart
17	chr2:86250800-86262200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:86251000-86253800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:86251000-86261000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:86251000-86262000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:86251000-86262600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:86251000-86262800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:86251200-86253800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:86251200-86254000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:86251200-86255000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr2:86251200-86255800	Genic enhancers	Fetal Thymus	thymus
27	chr2:86251200-86261600	Strong transcription	NH-A	brain
28	chr2:86251200-86261800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:86251200-86262400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:86251200-86262800	Strong transcription	Fetal Brain Female	brain
31	chr2:86251200-86263200	Strong transcription	A549	lung
32	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr2:86251200-86283000	Strong transcription	HepG2	liver
35	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:86251400-86253600	Weak transcription	Small Intestine	intestine
39	chr2:86251400-86254000	Weak transcription	Fetal Heart	heart
40	chr2:86251400-86254600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:86251400-86254600	Strong transcription	HSMMtube	muscle
42	chr2:86251400-86255800	Strong transcription	K562	blood
43	chr2:86251400-86261000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:86251400-86261000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:86251400-86261200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:86251400-86262000	Strong transcription	Osteobl	bone
47	chr2:86251400-86262800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:86251400-86263400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:86251600-86261600	Strong transcription	HMEC	breast
50	chr2:86251800-86259400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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