Variant report

Variant	rs7758978
Chromosome Location	chr6:35418442-35418443
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:35418420-35418570	NHLF	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35415818..35424678-chr6:35432486..35440672,36	K562	blood:
2	chr6:35309852..35312289-chr6:35417832..35421264,4	K562	blood:
3	chr6:35308697..35314051-chr6:35417510..35421585,8	K562	blood:
4	chr6:35292774..35294864-chr6:35417358..35419230,2	K562	blood:
5	chr6:35417496..35419930-chr6:35463187..35465266,3	MCF-7	breast:
6	chr6:35309295..35311429-chr6:35417090..35418674,2	MCF-7	breast:
7	chr6:35309118..35313462-chr6:35418133..35422102,7	MCF-7	breast:

No data

Variant related genes	Relation type
FANCE	TF binding region
ENSG00000112033	Chromatin interaction
ENSG00000007866	Chromatin interaction
ENSG00000198755	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10214770	0.96[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13214239	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2076170	0.92[CEU][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2395626	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6907678	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
4	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
5	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
6	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
7	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7758978	CPNE5	cis	cerebellum	SCAN
rs7758978	RPL10A	cis	multi-tissue	Pritchard
rs7758978	RPL10A	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35403400-35419400	Weak transcription	Right Atrium	heart
2	chr6:35406800-35419200	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:35411200-35419600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:35411400-35419400	Weak transcription	NHEK	skin
5	chr6:35411600-35419400	Weak transcription	HMEC	breast
6	chr6:35411800-35419200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:35413800-35419400	Weak transcription	Pancreas	Pancrea
8	chr6:35414000-35419200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:35414000-35419200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:35414200-35419000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:35414200-35419000	Weak transcription	Placenta	Placenta
12	chr6:35414200-35419600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:35414400-35419600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:35416400-35419200	Bivalent Enhancer	HepG2	liver
15	chr6:35416600-35419400	Weak transcription	Brain Substantia Nigra	brain
16	chr6:35417200-35419200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:35417400-35419000	Weak transcription	Dnd41	blood
18	chr6:35417600-35418800	Weak transcription	Adipose Nuclei	Adipose
19	chr6:35417600-35419000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:35417600-35419000	Weak transcription	Fetal Lung	lung
21	chr6:35417600-35419200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr6:35417600-35419200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:35417600-35419200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:35417600-35419200	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:35417600-35419200	Weak transcription	Right Ventricle	heart
26	chr6:35417600-35419200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:35417600-35419400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:35417600-35419400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:35417800-35418800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:35417800-35419000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:35417800-35419000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:35417800-35419000	Weak transcription	K562	blood
33	chr6:35417800-35419200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:35417800-35419200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:35417800-35419200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:35417800-35419200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:35417800-35419200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:35418000-35419400	Weak transcription	Brain Angular Gyrus	brain
39	chr6:35418000-35419400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:35418200-35419000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:35418400-35419200	Weak transcription	Brain Anterior Caudate	brain

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