Variant report

Variant	rs12530170
Chromosome Location	chr6:36623083-36623084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36562047..36564243-chr6:36622907..36625343,2	MCF-7	breast:
2	chr6:36617326..36619244-chr6:36622904..36626084,3	K562	blood:
3	chr6:36615853..36625488-chr6:36645022..36649146,15	MCF-7	breast:
4	chr6:36619841..36621635-chr6:36622788..36625137,2	K562	blood:
5	chr6:36619714..36621420-chr6:36622788..36625577,3	K562	blood:

Variant related genes	Relation type
ENSG00000124762	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10456441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059234	0.80[JPT][hapmap]
rs10807170	0.80[YRI][hapmap]
rs10947616	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947619	1.00[ASW][hapmap];0.84[CHD][hapmap];0.93[YRI][hapmap]
rs10947621	1.00[ASW][hapmap];0.84[CHD][hapmap];0.93[YRI][hapmap]
rs10947623	1.00[ASW][hapmap];0.84[CHD][hapmap];0.93[YRI][hapmap]
rs12203953	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12206430	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12210094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214686	1.00[ASW][hapmap];0.84[CHD][hapmap];0.93[YRI][hapmap]
rs12524435	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528248	0.85[JPT][hapmap]
rs12528913	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1801270	0.85[JPT][hapmap]
rs3829963	1.00[ASW][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4464789	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711460	0.80[AFR][1000 genomes]
rs4713993	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6457932	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6457934	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6915170	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6920453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931097	0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs72853320	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7382183	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7757749	0.85[JPT][hapmap]
rs7761648	0.85[JPT][hapmap]
rs876581	0.85[JPT][hapmap]
rs9349002	0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9349003	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349005	1.00[ASW][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9366912	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394371	0.82[AFR][1000 genomes];0.84[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	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12530170	CPNE5	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36611600-36628600	Weak transcription	Right Atrium	heart
2	chr6:36613400-36625000	Weak transcription	Fetal Kidney	kidney
3	chr6:36618200-36624600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:36618200-36627400	Weak transcription	Left Ventricle	heart
5	chr6:36619200-36625600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:36619400-36628400	Weak transcription	Adipose Nuclei	Adipose
7	chr6:36620200-36628000	Weak transcription	Colonic Mucosa	Colon
8	chr6:36620200-36628600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:36620400-36623200	Weak transcription	Primary B cells from cord blood	blood
10	chr6:36620400-36626200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:36621600-36624400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:36621800-36626000	Enhancers	Thymus	Thymus
13	chr6:36622000-36626200	Enhancers	Fetal Thymus	thymus
14	chr6:36622200-36628600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:36622400-36624200	Enhancers	Placenta	Placenta
16	chr6:36622400-36628800	Enhancers	GM12878-XiMat	blood
17	chr6:36622600-36623400	Enhancers	Fetal Intestine Small	intestine
18	chr6:36622800-36623200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:36622800-36623200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:36622800-36623400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:36622800-36623400	Enhancers	Fetal Muscle Leg	muscle
22	chr6:36623000-36623200	Enhancers	Colon Smooth Muscle	Colon
23	chr6:36623000-36623200	Enhancers	Fetal Heart	heart
24	chr6:36623000-36623200	Enhancers	NH-A	brain
25	chr6:36623000-36623400	Enhancers	Fetal Stomach	stomach
26	chr6:36623000-36623800	Bivalent Enhancer	Dnd41	blood
27	chr6:36623000-36625000	Weak transcription	Fetal Intestine Large	intestine

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