Variant report

Variant	rs12528712
Chromosome Location	chr6:109660884-109660885
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109660514..109663248-chr6:109671174..109674117,2	K562	blood:
2	chr6:109624816..109627658-chr6:109659263..109661556,2	K562	blood:
3	chr6:109655737..109658352-chr6:109659760..109662191,3	K562	blood:
4	chr6:109659415..109661984-chr6:109702237..109705687,4	MCF-7	breast:
5	chr6:109656032..109659893-chr6:109659967..109664099,6	MCF-7	breast:
6	chr6:109635700..109637262-chr6:109660535..109662631,2	K562	blood:
7	chr6:109571423..109573781-chr6:109659713..109661931,2	MCF-7	breast:
8	chr6:109660483..109663037-chr6:109663413..109665260,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260273	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000203799	Chromatin interaction
ENSG00000201023	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10457192	0.83[MKK][hapmap]
rs1048203	0.85[CEU][hapmap]
rs10782162	0.90[CEU][hapmap];0.93[MKK][hapmap]
rs11153174	0.85[CEU][hapmap]
rs11153175	0.85[CEU][hapmap]
rs11153183	0.83[MKK][hapmap]
rs11753645	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11757877	0.84[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11967108	0.85[CEU][hapmap]
rs12190920	0.85[CEU][hapmap]
rs12197114	0.85[CEU][hapmap]
rs12524502	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]
rs12524639	0.85[CEU][hapmap]
rs12528566	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12528822	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs13192476	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13195517	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13199519	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13203252	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13220304	0.89[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1322818	0.87[CEU][hapmap];0.91[AMR][1000 genomes]
rs1358998	0.85[CEU][hapmap]
rs17070580	0.81[CEU][hapmap]
rs1923725	0.85[CEU][hapmap]
rs2236582	0.80[CEU][hapmap]
rs2275650	0.85[CEU][hapmap]
rs2275652	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34131679	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34292461	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34320275	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35452836	0.82[EUR][1000 genomes]
rs35969918	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3757234	0.85[CEU][hapmap]
rs3757238	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3799835	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3799840	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61076041	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61233650	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61318425	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67857472	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6911838	0.81[CEU][hapmap]
rs6929208	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7773095	0.85[CEU][hapmap]
rs9320287	0.81[CEU][hapmap]
rs9480948	0.85[CEU][hapmap]
rs9480953	0.81[CEU][hapmap]
rs9480957	0.85[CEU][hapmap]
rs9487094	0.81[CEU][hapmap]
rs9487100	0.85[CEU][hapmap]
rs9885646	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12528712	SMPD2	cis	cerebellum	SCAN
rs12528712	PDSS2	cis	cerebellum	SCAN
rs12528712	CD164	cis	parietal	SCAN
rs12528712	AKD1	cis	cerebellum	SCAN
rs12528712	MICAL1	cis	parietal	SCAN
rs12528712	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs12528712	SMPD2	cis	parietal	SCAN
rs12528712	SMPD2	cis	multi-tissue	Pritchard
rs12528712	PPIL6	cis	cerebellum	SCAN
rs12528712	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12528712	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:42 , 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	chr6:109645400-109662400	Weak transcription	Aorta	Aorta
3	chr6:109654000-109669400	Weak transcription	Small Intestine	intestine
4	chr6:109654200-109671000	Weak transcription	Spleen	Spleen
5	chr6:109654200-109675000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:109654200-109676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:109654400-109668800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:109656800-109662600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:109657800-109661000	Weak transcription	Placenta	Placenta
10	chr6:109657800-109662200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:109657800-109662200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:109657800-109671000	Weak transcription	Lung	lung
13	chr6:109658000-109661400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:109658200-109661000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:109658200-109663600	Weak transcription	Left Ventricle	heart
16	chr6:109658400-109665200	Weak transcription	Fetal Intestine Small	intestine
17	chr6:109658400-109669200	Weak transcription	Liver	Liver
18	chr6:109658600-109661400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:109658600-109662200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:109658600-109662200	Weak transcription	Right Ventricle	heart
21	chr6:109658600-109668200	Weak transcription	Colonic Mucosa	Colon
22	chr6:109658600-109670600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:109658800-109661000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:109658800-109661000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:109658800-109662000	Weak transcription	Adipose Nuclei	Adipose
26	chr6:109658800-109663600	Weak transcription	Gastric	stomach
27	chr6:109658800-109663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:109658800-109670600	Weak transcription	Right Atrium	heart
29	chr6:109658800-109677000	Weak transcription	Fetal Stomach	stomach
30	chr6:109659000-109661400	Weak transcription	Stomach Mucosa	stomach
31	chr6:109659400-109661200	Enhancers	K562	blood
32	chr6:109660200-109661400	Enhancers	Fetal Thymus	thymus
33	chr6:109660200-109677200	Weak transcription	Thymus	Thymus
34	chr6:109660400-109661200	Enhancers	Pancreas	Pancrea
35	chr6:109660400-109662000	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr6:109660400-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:109660600-109665800	Enhancers	Fetal Muscle Leg	muscle
38	chr6:109660600-109666000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:109660800-109661200	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr6:109660800-109661200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr6:109660800-109661600	Enhancers	Primary hematopoietic stem cells	blood
42	chr6:109660800-109666000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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