Variant report

Variant	rs12530178
Chromosome Location	chr6:144018119-144018120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144018054..144020954-chr6:144022528..144024554,3	MCF-7	breast:
2	chr6:143831227..143833944-chr6:144017748..144020555,2	MCF-7	breast:
3	chr6:144015602..144018341-chr6:144021601..144023244,2	K562	blood:
4	chr6:144004544..144009046-chr6:144017005..144020189,4	K562	blood:
5	chr6:144011351..144015622-chr6:144016784..144019989,3	K562	blood:

Variant related genes	Relation type
ENSG00000001036	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11755709	0.91[ASN][1000 genomes]
rs12199447	0.91[ASN][1000 genomes]
rs12200809	0.86[ASN][1000 genomes]
rs12524982	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12525281	0.84[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12525974	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12527275	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12528079	0.80[AMR][1000 genomes]
rs13192672	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13193972	0.91[ASN][1000 genomes]
rs13194278	1.00[CHB][hapmap]
rs13199178	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13213692	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13214196	0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13219740	0.86[ASN][1000 genomes]
rs17291151	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1884172	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2051009	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2328507	0.90[CHB][hapmap]
rs34775537	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62427376	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62427377	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6932482	0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7744358	1.00[CHB][hapmap]
rs7760627	1.00[CHB][hapmap]
rs9484792	1.00[CHB][hapmap]
rs9484795	0.89[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9496738	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9496740	0.89[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv886737	chr6:144010570-144033992	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144005000-144020400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:144010200-144019600	Weak transcription	Spleen	Spleen
3	chr6:144010400-144020000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:144011600-144053200	Weak transcription	Hela-S3	cervix
5	chr6:144011800-144019600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:144011800-144019800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:144012200-144018600	Enhancers	Stomach Mucosa	stomach
8	chr6:144012200-144026800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:144013800-144019200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr6:144014000-144019600	Weak transcription	Placenta	Placenta
11	chr6:144014200-144018200	Enhancers	Stomach Smooth Muscle	stomach
12	chr6:144014200-144019800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:144014200-144019800	Weak transcription	Right Atrium	heart
14	chr6:144014200-144027800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:144014200-144039800	Weak transcription	Pancreas	Pancrea
16	chr6:144014400-144019000	Enhancers	HepG2	liver
17	chr6:144014400-144022600	Weak transcription	Fetal Intestine Large	intestine
18	chr6:144014600-144020200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:144014800-144018200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:144014800-144019000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr6:144014800-144020800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr6:144015000-144018200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:144015000-144018200	Enhancers	Fetal Muscle Leg	muscle
24	chr6:144015000-144018400	Enhancers	Fetal Lung	lung
25	chr6:144015000-144019800	Enhancers	Colon Smooth Muscle	Colon
26	chr6:144015200-144018800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:144015400-144019800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:144015400-144019800	Weak transcription	Gastric	stomach
29	chr6:144015400-144020000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:144015400-144020800	Weak transcription	Lung	lung
31	chr6:144015400-144034600	Weak transcription	Esophagus	oesophagus
32	chr6:144015600-144018200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:144015600-144018200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:144015600-144018200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr6:144015800-144021800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:144016000-144018400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr6:144016000-144018600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr6:144016000-144021800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:144016000-144022000	Weak transcription	HSMMtube	muscle
40	chr6:144016200-144019600	Weak transcription	HSMM	muscle
41	chr6:144016200-144021600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr6:144016200-144023000	Enhancers	Adipose Nuclei	Adipose
43	chr6:144016200-144037200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:144016200-144038000	Weak transcription	NHEK	skin
45	chr6:144016400-144019800	Weak transcription	Left Ventricle	heart
46	chr6:144016400-144022000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:144016600-144018600	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr6:144016600-144019800	Weak transcription	Right Ventricle	heart
49	chr6:144016600-144020000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:144016600-144034000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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