Variant report

Variant	rs6966465
Chromosome Location	chr7:28013603-28013604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17156085	1.00[JPT][hapmap]
rs17695685	0.92[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2106922	0.96[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs34079332	0.86[EUR][1000 genomes]
rs34714526	0.85[EUR][1000 genomes]
rs3857729	0.83[EUR][1000 genomes]
rs763896	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs9648343	0.82[CEU][hapmap];0.85[EUR][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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1024819	chr7:27949955-28020969	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6966465	HOXA4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27980400-28017200	Weak transcription	Aorta	Aorta
2	chr7:27998400-28015000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr7:28000600-28019400	Weak transcription	Pancreas	Pancrea
4	chr7:28000600-28021600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:28002600-28016800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:28002800-28034600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:28006200-28015600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:28006200-28019200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:28006200-28024800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:28006400-28031800	Weak transcription	NHDF-Ad	bronchial
11	chr7:28006600-28016000	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:28007000-28019200	Weak transcription	Esophagus	oesophagus
13	chr7:28009800-28021600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr7:28011800-28014200	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr7:28012200-28014000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:28012200-28014800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:28012400-28013800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr7:28012400-28014000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr7:28012400-28014800	Weak transcription	Thymus	Thymus
20	chr7:28012400-28022200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:28012400-28028000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr7:28013000-28014000	Enhancers	Brain Angular Gyrus	brain
23	chr7:28013000-28014400	Enhancers	Brain Substantia Nigra	brain
24	chr7:28013400-28014000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:28013400-28014000	Enhancers	Brain Anterior Caudate	brain
26	chr7:28013400-28014000	Enhancers	Brain Cingulate Gyrus	brain
27	chr7:28013400-28014000	Enhancers	Left Ventricle	heart
28	chr7:28013400-28014400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:28013400-28014400	Enhancers	Brain Hippocampus Middle	brain
30	chr7:28013400-28020000	Strong transcription	Primary B cells from cord blood	blood
31	chr7:28013400-28034200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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