Variant report

Variant	rs12470643
Chromosome Location	chr2:86183224-86183225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86112745..86122516-chr2:86175080..86185190,27	MCF-7	breast:
2	chr2:86170585..86172715-chr2:86181758..86183932,2	MCF-7	breast:
3	chr2:86181209..86184209-chr2:86184954..86187247,3	K562	blood:
4	chr2:86135754..86137623-chr2:86180466..86183254,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232504	Chromatin interaction
ENSG00000115525	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10181091	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10181916	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10183118	0.84[EUR][1000 genomes]
rs10186005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189191	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198260	0.92[ASN][1000 genomes]
rs1020095	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11890514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472588	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476390	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714161	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12714163	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714164	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12714165	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13000793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13397189	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1438153	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1438155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561330	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866242	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866243	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1866245	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4346389	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4480982	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4514874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832018	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4832020	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6547651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706720	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708525	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713002	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6728146	0.80[EUR][1000 genomes]
rs6737454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597264	0.87[ASN][1000 genomes]
rs934830	0.85[EUR][1000 genomes];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12470643	IMMT	cis	uninvolved skin	skin_eQTL
rs12470643	IMMT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86175000-86183600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:86178800-86188200	Enhancers	Fetal Muscle Leg	muscle
3	chr2:86179200-86183600	Enhancers	Pancreas	Pancrea
4	chr2:86179200-86183800	Enhancers	Stomach Mucosa	stomach
5	chr2:86180000-86183400	Enhancers	Fetal Muscle Trunk	muscle
6	chr2:86180200-86187600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:86180600-86184200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:86180800-86184000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:86180800-86184400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:86180800-86188600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:86181000-86183600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:86181000-86183800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:86181000-86186600	Weak transcription	K562	blood
14	chr2:86181800-86184200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:86181800-86186200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:86182000-86183400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:86182200-86183400	Enhancers	NHEK	skin
18	chr2:86182400-86184400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:86182600-86183400	Enhancers	A549	lung
20	chr2:86182600-86187600	Weak transcription	Esophagus	oesophagus
21	chr2:86183000-86184200	Enhancers	HMEC	breast
22	chr2:86183000-86184400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:86183000-86184600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr2:86183000-86184600	Enhancers	HSMM	muscle
25	chr2:86183000-86184800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:86183200-86183400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr2:86183200-86184400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:86183200-86184600	Enhancers	HSMMtube	muscle

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