Variant report

Variant	rs10946968
Chromosome Location	chr6:11128299-11128300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11092497..11095827-chr6:11127502..11129966,4	MCF-7	breast:
2	chr1:208405165..208405665-chr6:11128040..11128541,2	NB4	blood:

Variant related genes	Relation type
ENSG00000224531	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10484446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484448	0.88[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10946967	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947002	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11751998	0.88[CEU][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11759939	0.87[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12190970	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193702	1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12194681	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12199551	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12200717	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200932	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205389	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211539	0.82[CEU][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12212683	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12213689	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12215910	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711180	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6456846	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906952	1.00[JPT][hapmap]

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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10946968	EDN1	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11095600-11135200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:11101600-11134800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:11112400-11128400	Weak transcription	Spleen	Spleen
4	chr6:11112400-11134600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:11112400-11135000	Weak transcription	Primary T cells from cord blood	blood
6	chr6:11112400-11135400	Weak transcription	Thymus	Thymus
7	chr6:11112400-11137200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:11112600-11134600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:11112600-11134600	Weak transcription	Dnd41	blood
10	chr6:11112600-11135000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:11116600-11144000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:11120600-11134600	Weak transcription	Fetal Thymus	thymus
13	chr6:11120600-11136800	Weak transcription	Brain Germinal Matrix	brain
14	chr6:11120800-11134600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:11121000-11130000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:11121200-11129800	Weak transcription	NHDF-Ad	bronchial
17	chr6:11121200-11130000	Weak transcription	GM12878-XiMat	blood
18	chr6:11121200-11134800	Weak transcription	HMEC	breast
19	chr6:11121200-11135200	Weak transcription	HSMMtube	muscle
20	chr6:11121200-11136800	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:11121400-11130000	Weak transcription	NHEK	skin
22	chr6:11121400-11130200	Weak transcription	HUVEC	blood vessel
23	chr6:11121400-11135000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:11121600-11135000	Weak transcription	Fetal Lung	lung
25	chr6:11122400-11128600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:11122400-11134800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:11122600-11130800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:11122600-11134800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:11122600-11135000	Weak transcription	Adipose Nuclei	Adipose
30	chr6:11122800-11130400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:11122800-11130600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:11123000-11130000	Weak transcription	A549	lung
33	chr6:11123000-11135000	Weak transcription	Hela-S3	cervix
34	chr6:11123000-11135400	Weak transcription	Ovary	ovary
35	chr6:11123200-11128600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:11123400-11130200	Weak transcription	Small Intestine	intestine
37	chr6:11123600-11134600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:11123600-11134800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:11123600-11135000	Weak transcription	K562	blood
40	chr6:11124200-11134800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:11125000-11134600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:11125000-11134800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:11125200-11134800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:11125400-11135000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr6:11125800-11128800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:11126200-11135000	Weak transcription	Placenta	Placenta
47	chr6:11126400-11134600	Weak transcription	Fetal Intestine Large	intestine
48	chr6:11126800-11128800	Genic enhancers	HepG2	liver
49	chr6:11126800-11129200	Enhancers	Brain Cingulate Gyrus	brain
50	chr6:11126800-11134600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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