Variant report

Variant	rs12997506
Chromosome Location	chr2:86254268-86254269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86253744..86255474-chr2:86257565..86259502,2	MCF-7	breast:
2	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: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10178120	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10178540	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10185452	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10198260	0.80[ASN][1000 genomes]
rs12714162	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12714164	0.80[ASN][1000 genomes]
rs12714165	0.80[ASN][1000 genomes]
rs12714166	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12994838	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13004643	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13024123	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278536	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289239	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34478066	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34723687	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770075	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4597526	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4832018	0.80[ASN][1000 genomes]
rs4832019	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4832020	0.80[ASN][1000 genomes]
rs4832234	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832236	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6735014	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6740044	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7572386	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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 miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12997506	IMMT	cis	multi-tissue	Pritchard
rs12997506	IMMT	cis	Whole Blood	GTEx
rs12997506	IMMT	cis	Esophagus Muscularis	GTEx
rs12997506	LOC90784	Cis_1M	lymphoblastoid	RTeQTL
rs12997506	IMMT	cis	Artery Aorta	GTEx
rs12997506	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs12997506	IMMT	Cis_1M	lymphoblastoid	RTeQTL

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	chr2:86245400-86254600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:86245400-86257200	Weak transcription	Stomach Mucosa	stomach
7	chr2:86245400-86257400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:86245400-86263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:86248800-86257000	Weak transcription	Psoas Muscle	Psoas
10	chr2:86248800-86257200	Weak transcription	Fetal Kidney	kidney
11	chr2:86249000-86255200	Weak transcription	Right Atrium	heart
12	chr2:86250800-86262200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:86251000-86261000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:86251000-86262000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:86251000-86262600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:86251000-86262800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:86251200-86255000	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr2:86251200-86255800	Genic enhancers	Fetal Thymus	thymus
19	chr2:86251200-86261600	Strong transcription	NH-A	brain
20	chr2:86251200-86261800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:86251200-86262400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:86251200-86262800	Strong transcription	Fetal Brain Female	brain
23	chr2:86251200-86263200	Strong transcription	A549	lung
24	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr2:86251200-86283000	Strong transcription	HepG2	liver
27	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:86251400-86254600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr2:86251400-86254600	Strong transcription	HSMMtube	muscle
32	chr2:86251400-86255800	Strong transcription	K562	blood
33	chr2:86251400-86261000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:86251400-86261000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:86251400-86261200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:86251400-86262000	Strong transcription	Osteobl	bone
37	chr2:86251400-86262800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:86251400-86263400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:86251600-86261600	Strong transcription	HMEC	breast
40	chr2:86251800-86259400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:86251800-86262000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:86251800-86262400	Strong transcription	Fetal Intestine Small	intestine
43	chr2:86252000-86254600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:86252000-86262000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:86252200-86262000	Strong transcription	GM12878-XiMat	blood
47	chr2:86252200-86262400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:86252200-86262600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell

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