Variant report

Variant	rs12524502
Chromosome Location	chr6:109654221-109654222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109649495..109651298-chr6:109651628..109654623,3	K562	blood:
2	chr6:109654193..109659063-chr6:109701671..109705275,8	MCF-7	breast:
3	chr6:109652681..109655937-chr6:109701274..109703936,3	MCF-7	breast:
4	chr6:109652928..109655072-chr6:109655937..109657890,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260273	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1048203	0.81[CEU][hapmap]
rs10782162	0.85[CEU][hapmap]
rs11753645	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11757877	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12528566	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12528712	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528822	0.81[CEU][hapmap]
rs13192476	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13195517	0.95[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13199519	0.85[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13203252	0.94[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13220304	0.95[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1322818	0.82[CEU][hapmap]
rs1358998	0.81[CEU][hapmap]
rs2275650	0.81[CEU][hapmap]
rs2275652	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34131679	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34292461	0.81[EUR][1000 genomes]
rs34320275	0.90[EUR][1000 genomes]
rs35452836	0.81[EUR][1000 genomes]
rs35969918	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3757238	0.89[EUR][1000 genomes]
rs3799835	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799840	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61076041	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61233650	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61318425	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67857472	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6929208	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7773095	0.81[CEU][hapmap]
rs9480948	0.81[CEU][hapmap]
rs9480957	0.81[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12524502	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs12524502	SMPD2	cis	Whole Blood	GTEx
rs12524502	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12524502	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12524502	RP11-425D10.10	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:109644800-109657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:109645400-109662400	Weak transcription	Aorta	Aorta
4	chr6:109651600-109654600	Enhancers	Stomach Mucosa	stomach
5	chr6:109653000-109655000	Enhancers	Fetal Intestine Large	intestine
6	chr6:109653000-109655000	Enhancers	Fetal Intestine Small	intestine
7	chr6:109653000-109655000	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr6:109653400-109654400	Enhancers	Duodenum Mucosa	Duodenum
9	chr6:109653400-109654400	Active TSS	Rectal Smooth Muscle	rectum
10	chr6:109653400-109654400	Enhancers	Right Ventricle	heart
11	chr6:109653400-109658800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr6:109653600-109654400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:109653600-109654400	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr6:109653600-109654600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:109653600-109654600	Enhancers	HepG2	liver
16	chr6:109653800-109654400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr6:109653800-109654400	Enhancers	Esophagus	oesophagus
18	chr6:109653800-109654400	Enhancers	Gastric	stomach
19	chr6:109653800-109654400	Enhancers	Lung	lung
20	chr6:109653800-109654400	Enhancers	Hela-S3	cervix
21	chr6:109653800-109656400	Weak transcription	Colonic Mucosa	Colon
22	chr6:109654000-109654400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:109654000-109654400	Enhancers	Fetal Muscle Leg	muscle
24	chr6:109654000-109654400	Enhancers	Placenta	Placenta
25	chr6:109654000-109654400	Enhancers	K562	blood
26	chr6:109654000-109657400	Weak transcription	Pancreas	Pancrea
27	chr6:109654000-109657600	Weak transcription	Adipose Nuclei	Adipose
28	chr6:109654000-109669400	Weak transcription	Small Intestine	intestine
29	chr6:109654200-109654400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:109654200-109657000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:109654200-109657400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:109654200-109671000	Weak transcription	Spleen	Spleen
33	chr6:109654200-109675000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr6:109654200-109676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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