Variant report

Variant	rs11969445
Chromosome Location	chr6:36625382-36625383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36617326..36619244-chr6:36622904..36626084,3	K562	blood:
2	chr6:36615853..36625488-chr6:36645022..36649146,15	MCF-7	breast:
3	chr6:36619714..36621420-chr6:36622788..36625577,3	K562	blood:
4	chr6:36623725..36625807-chr6:36629087..36632013,3	K562	blood:

Variant related genes	Relation type
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs4568449	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457931	0.81[CHD][hapmap]
rs6457933	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6907437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936598	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936993	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9462209	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9470362	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9470363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	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
3	esv3448277	chr6:36625374-36628672	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11969445	MDGA1	cis	cerebellum	SCAN
rs11969445	FLJ43093	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36611600-36628600	Weak transcription	Right Atrium	heart
2	chr6:36618200-36627400	Weak transcription	Left Ventricle	heart
3	chr6:36619200-36625600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:36619400-36628400	Weak transcription	Adipose Nuclei	Adipose
5	chr6:36620200-36628000	Weak transcription	Colonic Mucosa	Colon
6	chr6:36620200-36628600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:36620400-36626200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:36621800-36626000	Enhancers	Thymus	Thymus
9	chr6:36622000-36626200	Enhancers	Fetal Thymus	thymus
10	chr6:36622200-36628600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:36622400-36628800	Enhancers	GM12878-XiMat	blood
12	chr6:36623200-36625600	Weak transcription	NH-A	brain
13	chr6:36623200-36628600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:36623400-36625400	Weak transcription	Fetal Intestine Small	intestine
15	chr6:36623400-36625400	Weak transcription	Fetal Stomach	stomach
16	chr6:36623400-36626000	Weak transcription	Fetal Heart	heart
17	chr6:36623400-36628800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:36623600-36626200	Weak transcription	Primary B cells from cord blood	blood
19	chr6:36624600-36627800	Enhancers	Placenta	Placenta
20	chr6:36624600-36628800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:36624800-36627400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:36625000-36625600	Enhancers	Fetal Kidney	kidney
23	chr6:36625000-36626200	Enhancers	Fetal Intestine Large	intestine
24	chr6:36625000-36627600	Enhancers	Rectal Smooth Muscle	rectum
25	chr6:36625000-36628000	Enhancers	Osteobl	bone
26	chr6:36625000-36628200	Enhancers	Colon Smooth Muscle	Colon
27	chr6:36625000-36628800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:36625200-36625600	Bivalent Enhancer	HepG2	liver
29	chr6:36625200-36627000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:36625200-36627200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:36625200-36627800	Enhancers	HMEC	breast

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