Variant report

Variant	rs1621496
Chromosome Location	chr10:61629823-61629824
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:61628076..61632189-chr10:61632717..61638646,7	K562	blood:
2	chr10:61629487..61632652-chr10:61653201..61655969,3	K562	blood:
3	chr10:61627957..61629887-chr10:61630516..61633245,2	MCF-7	breast:
4	chr10:61611168..61612736-chr10:61629304..61631288,2	K562	blood:
5	chr10:61628053..61630048-chr10:61661857..61663658,2	K562	blood:
6	chr10:61628363..61632189-chr10:61637394..61643761,6	K562	blood:
7	chr10:61628053..61631509-chr10:61662158..61666953,4	K562	blood:
8	chr10:61593326..61595203-chr10:61629041..61631124,2	K562	blood:
9	chr10:61628330..61633371-chr10:61664622..61667776,4	MCF-7	breast:
10	chr10:61628499..61631972-chr10:61632717..61636046,5	K562	blood:
11	chr10:61629487..61631429-chr10:61653201..61655597,2	K562	blood:
12	chr10:61623680..61630815-chr10:61664299..61668134,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10458645	0.85[JPT][hapmap]
rs10821604	0.86[JPT][hapmap]
rs10821607	0.86[JPT][hapmap]
rs10994026	0.80[JPT][hapmap]
rs10994027	0.80[JPT][hapmap]
rs10994031	0.80[JPT][hapmap]
rs10994051	0.90[ASN][1000 genomes]
rs1149660	0.84[JPT][hapmap]
rs1149661	0.80[ASN][1000 genomes]
rs1149662	0.80[ASN][1000 genomes]
rs1171786	0.89[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1171788	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1177701	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12243564	0.81[CEU][hapmap];0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs12266466	0.84[ASN][1000 genomes]
rs1626088	0.82[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1664255	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1664284	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1664285	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1684896	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684901	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1709342	0.84[JPT][hapmap]
rs1709343	0.85[JPT][hapmap]
rs1709345	0.89[JPT][hapmap]
rs1871637	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1871638	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2120989	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2120990	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2271562	0.82[JPT][hapmap]
rs2440926	0.85[JPT][hapmap]
rs2458661	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs2458663	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3106569	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3844161	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3851247	0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs3851248	0.93[ASN][1000 genomes]
rs3862860	0.92[ASN][1000 genomes]
rs3862861	0.93[ASN][1000 genomes]
rs3999569	0.82[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3999570	0.81[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4948372	0.81[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4948373	0.93[ASN][1000 genomes]
rs4948374	0.85[JPT][hapmap]
rs4948375	0.84[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs55842846	0.89[ASN][1000 genomes]
rs61848702	0.92[ASN][1000 genomes]
rs6479654	0.86[JPT][hapmap]
rs6479657	0.84[ASN][1000 genomes]
rs6479659	0.89[ASN][1000 genomes]
rs6479660	0.87[ASN][1000 genomes]
rs6479661	0.82[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6479662	0.93[ASN][1000 genomes]
rs7068104	0.89[ASN][1000 genomes]
rs7068247	0.93[ASN][1000 genomes]
rs7070800	0.92[ASN][1000 genomes]
rs7074685	0.93[ASN][1000 genomes]
rs7079228	0.81[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7088755	0.80[JPT][hapmap]
rs7088808	0.92[ASN][1000 genomes]
rs7088886	0.85[JPT][hapmap]
rs7092259	0.80[JPT][hapmap]
rs7908517	0.85[JPT][hapmap]
rs7920403	0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9663498	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs9664183	0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1621496	CCDC6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:93 , 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	chr10:61608000-61637200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:61618000-61632600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr10:61618600-61633200	Weak transcription	HSMM	muscle
5	chr10:61621200-61630200	Weak transcription	Fetal Stomach	stomach
6	chr10:61624200-61630400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr10:61624400-61630400	Enhancers	Pancreas	Pancrea
8	chr10:61624400-61632000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:61624600-61631200	Weak transcription	Fetal Lung	lung
10	chr10:61624800-61633000	Weak transcription	Brain Germinal Matrix	brain
11	chr10:61624800-61641000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr10:61625000-61632000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr10:61625000-61632000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr10:61625000-61632600	Weak transcription	Ovary	ovary
15	chr10:61625000-61638800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:61625000-61655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:61625200-61631600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr10:61625200-61632000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:61625200-61639200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr10:61625400-61631600	Weak transcription	Primary B cells from cord blood	blood
21	chr10:61625400-61631600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr10:61625600-61631400	Weak transcription	GM12878-XiMat	blood
23	chr10:61625600-61631600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr10:61625800-61632600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr10:61626000-61631600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr10:61626000-61631800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr10:61626000-61632200	Weak transcription	NHEK	skin
28	chr10:61626000-61632400	Weak transcription	Adipose Nuclei	Adipose
29	chr10:61626200-61631400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr10:61626400-61631400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr10:61626400-61632000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:61626600-61631800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:61626800-61630400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr10:61626800-61631400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:61627000-61631600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr10:61627000-61632600	Weak transcription	Brain Substantia Nigra	brain
37	chr10:61627400-61630400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr10:61627600-61630000	Enhancers	Primary B cells from peripheral blood	blood
39	chr10:61627800-61630000	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr10:61627800-61630400	Enhancers	Duodenum Mucosa	Duodenum
41	chr10:61628000-61630000	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr10:61628000-61630600	Enhancers	Gastric	stomach
43	chr10:61628000-61630800	Enhancers	Brain Anterior Caudate	brain
44	chr10:61628400-61630000	Enhancers	Fetal Intestine Small	intestine
45	chr10:61628400-61630000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr10:61628400-61630800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr10:61628400-61632400	Enhancers	Colon Smooth Muscle	Colon
48	chr10:61628600-61631400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr10:61628600-61632800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr10:61628600-61632800	Enhancers	K562	blood

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