Variant report

Variant	rs1626088
Chromosome Location	chr10:61640320-61640321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:61638398..61641573-chr10:61642787..61646612,4	K562	blood:
2	chr10:61636740..61643413-chr10:61643807..61649213,6	K562	blood:
3	chr10:61639063..61643015-chr10:61647185..61650219,3	MCF-7	breast:
4	chr10:61628363..61632189-chr10:61637394..61643761,6	K562	blood:
5	chr10:61638896..61642309-chr10:61665188..61667493,3	K562	blood:
6	chr10:61640293..61643125-chr10:61664795..61666558,2	MCF-7	breast:
7	chr10:61633677..61637740-chr10:61638115..61642166,4	K562	blood:
8	chr10:61635533..61637804-chr10:61638300..61641205,3	K562	blood:
9	chr10:61639233..61641192-chr10:61644964..61647007,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1171786	0.89[CEU][hapmap];0.82[GIH][hapmap];0.84[EUR][1000 genomes]
rs1171788	0.86[EUR][1000 genomes]
rs1171812	0.82[GIH][hapmap];0.91[JPT][hapmap]
rs1171830	0.80[MEX][hapmap]
rs1177701	0.87[ASW][hapmap];0.82[CEU][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.89[TSI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1184593	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs1621496	0.82[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1664255	0.88[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1664256	0.89[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.85[EUR][1000 genomes]
rs1684896	0.90[EUR][1000 genomes]
rs1684901	0.89[GIH][hapmap]
rs2440907	0.84[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	esv1795420	chr10:61637271-61669227	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
2	esv1800316	chr10:61639599-61700473	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	esv3436809	chr10:61640046-61644344	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1626088	CCDC6	cis	Esophagus Mucosa	GTEx
rs1626088	SLC16A9	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61583200-61640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:61624800-61641000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:61625000-61655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:61630000-61647800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:61633000-61640600	Weak transcription	Gastric	stomach
6	chr10:61633200-61640600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:61633200-61641800	Weak transcription	Lung	lung
8	chr10:61633400-61643200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr10:61633400-61645200	Weak transcription	Fetal Thymus	thymus
10	chr10:61633400-61647800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:61633400-61647800	Weak transcription	Fetal Muscle Leg	muscle
12	chr10:61633400-61647800	Weak transcription	Fetal Stomach	stomach
13	chr10:61633400-61648600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr10:61633600-61645200	Weak transcription	Brain Germinal Matrix	brain
15	chr10:61634000-61640400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr10:61634000-61645000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr10:61634000-61645600	Weak transcription	Fetal Lung	lung
18	chr10:61634000-61646800	Weak transcription	Adipose Nuclei	Adipose
19	chr10:61634400-61648800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:61634400-61649000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr10:61634400-61651200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr10:61634600-61640600	Weak transcription	Left Ventricle	heart
23	chr10:61634800-61640600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:61634800-61645200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr10:61635000-61644000	Weak transcription	Brain Angular Gyrus	brain
26	chr10:61635000-61645400	Weak transcription	Brain Substantia Nigra	brain
27	chr10:61635000-61646800	Weak transcription	Right Ventricle	heart
28	chr10:61635400-61640800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:61635600-61640600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr10:61635600-61640600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr10:61635600-61640800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr10:61635600-61640800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr10:61635600-61647600	Weak transcription	Brain Anterior Caudate	brain
34	chr10:61635800-61640800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr10:61635800-61641000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:61635800-61648600	Enhancers	Primary B cells from peripheral blood	blood
37	chr10:61636200-61641800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr10:61636600-61641800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr10:61636800-61640600	Weak transcription	Fetal Intestine Small	intestine
40	chr10:61637000-61642200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr10:61637400-61641800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr10:61637400-61641800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr10:61637400-61645400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr10:61637400-61647800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:61637400-61648400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:61637600-61640400	Weak transcription	Primary B cells from cord blood	blood
47	chr10:61637600-61645200	Weak transcription	Right Atrium	heart
48	chr10:61637600-61653600	Weak transcription	NHDF-Ad	bronchial
49	chr10:61637800-61640600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr10:61637800-61645800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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