Variant report

Variant	rs6547651
Chromosome Location	chr2:86184486-86184487
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	chr2:86112745..86122516-chr2:86175080..86185190,27	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232504	Chromatin interaction
ENSG00000115525	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10181091	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10181916	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10183118	0.82[EUR][1000 genomes]
rs10186005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189191	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198260	0.92[ASN][1000 genomes]
rs1020095	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11890514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470643	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]
rs12472588	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476390	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714161	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12714163	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714164	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12714165	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13000793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13397189	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1438153	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561330	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866242	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866243	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1866245	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4346389	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4480982	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4514874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832018	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4832020	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6706720	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708525	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713002	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6737454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597264	0.87[ASN][1000 genomes]
rs934830	0.81[AMR][1000 genomes];0.83[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
rs6547651	IMMT	cis	uninvolved skin	skin_eQTL
rs6547651	IMMT	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86178800-86188200	Enhancers	Fetal Muscle Leg	muscle
2	chr2:86180200-86187600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:86180800-86188600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:86181000-86186600	Weak transcription	K562	blood
5	chr2:86181800-86186200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:86182600-86187600	Weak transcription	Esophagus	oesophagus
7	chr2:86183000-86184600	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr2:86183000-86184600	Enhancers	HSMM	muscle
9	chr2:86183000-86184800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:86183200-86184600	Enhancers	HSMMtube	muscle
11	chr2:86183400-86184600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:86183400-86184600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:86183400-86184800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:86183400-86185000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr2:86183400-86185200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:86183400-86185800	Weak transcription	A549	lung
17	chr2:86183600-86184600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr2:86183600-86184800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr2:86183600-86184800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr2:86183600-86187600	Weak transcription	Pancreas	Pancrea
21	chr2:86183800-86184600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr2:86183800-86184600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr2:86183800-86190800	Weak transcription	Stomach Mucosa	stomach
24	chr2:86184000-86184600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:86184000-86184600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr2:86184000-86184600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:86184000-86184800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr2:86184000-86184800	Enhancers	H9 Cell Line	embryonic stem cell
29	chr2:86184200-86184800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:86184200-86186600	Weak transcription	Psoas Muscle	Psoas
31	chr2:86184400-86184600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:86184400-86184600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:86184400-86184800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:86184400-86187600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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