Variant report

Variant	rs6543652
Chromosome Location	chr2:32400764-32400765
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	chr2:32389694..32394396-chr2:32399001..32405946,7	MCF-7	breast:
2	chr2:32390601..32394000-chr2:32400029..32402165,3	K562	blood:

Variant related genes	Relation type
ENSG00000272716	Chromatin interaction
ENSG00000152683	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13010978	1.00[CHD][hapmap]
rs2116030	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs212709	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs212719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs212750	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs216537	1.00[YRI][hapmap]
rs2365556	1.00[AMR][1000 genomes]
rs420225	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs420731	1.00[LWK][hapmap]
rs483796	1.00[CEU][hapmap]
rs533970	1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap]
rs552555	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs631826	1.00[CEU][hapmap]
rs6543650	1.00[CEU][hapmap]
rs6543651	0.87[ASW][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap]
rs7593078	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32391400-32401800	Weak transcription	Spleen	Spleen
2	chr2:32391400-32402000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:32391400-32402000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:32391600-32401800	Weak transcription	Gastric	stomach
5	chr2:32391600-32402000	Weak transcription	Esophagus	oesophagus
6	chr2:32391600-32402800	Weak transcription	Lung	lung
7	chr2:32391600-32403400	Weak transcription	Aorta	Aorta
8	chr2:32391600-32406600	Weak transcription	Small Intestine	intestine
9	chr2:32391600-32409600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:32391600-32426400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:32391600-32452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:32391800-32401800	Weak transcription	Brain Substantia Nigra	brain
13	chr2:32391800-32409600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:32391800-32431400	Weak transcription	Stomach Mucosa	stomach
15	chr2:32391800-32453800	Weak transcription	Colonic Mucosa	Colon
16	chr2:32392000-32401800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:32392000-32401800	Weak transcription	Brain Angular Gyrus	brain
18	chr2:32392000-32401800	Weak transcription	Fetal Stomach	stomach
19	chr2:32392000-32402000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:32392000-32402000	Weak transcription	Fetal Lung	lung
21	chr2:32392000-32402000	Weak transcription	Thymus	Thymus
22	chr2:32392000-32402200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:32392000-32403600	Weak transcription	Fetal Kidney	kidney
24	chr2:32392000-32403800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:32392000-32403800	Weak transcription	HSMMtube	muscle
26	chr2:32392000-32414600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:32392000-32435800	Weak transcription	NHLF	lung
28	chr2:32392200-32402000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:32392200-32402000	Weak transcription	Brain Germinal Matrix	brain
30	chr2:32392200-32402200	Weak transcription	Osteobl	bone
31	chr2:32392200-32403600	Weak transcription	HUVEC	blood vessel
32	chr2:32392200-32411600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:32392200-32422800	Weak transcription	Fetal Brain Male	brain
34	chr2:32392200-32445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:32392400-32402000	Weak transcription	Pancreas	Pancrea
36	chr2:32392800-32400800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:32392800-32410000	Weak transcription	Hela-S3	cervix
38	chr2:32392800-32447600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:32393000-32412400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:32393200-32402200	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:32395400-32405600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:32396000-32403800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:32396000-32414000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:32396200-32404800	Strong transcription	Dnd41	blood
45	chr2:32396200-32405600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:32396200-32413600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:32396400-32401000	Weak transcription	GM12878-XiMat	blood
48	chr2:32396400-32404400	Strong transcription	HepG2	liver
49	chr2:32396800-32405200	Strong transcription	Fetal Muscle Leg	muscle
50	chr2:32397000-32400800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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