Variant report

Variant	rs1664257
Chromosome Location	chr10:61631763-61631764
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:61628076..61632189-chr10:61632717..61638646,7	K562	blood:
2	chr10:61631763..61634620-chr10:61659289..61660920,2	MCF-7	breast:
3	chr10:61629487..61632652-chr10:61653201..61655969,3	K562	blood:
4	chr10:61630214..61632918-chr10:61637567..61639312,2	MCF-7	breast:
5	chr10:61631384..61634848-chr10:61664834..61667747,10	MCF-7	breast:
6	chr10:61630078..61632932-chr10:61659731..61661689,2	MCF-7	breast:
7	chr10:61628363..61632189-chr10:61637394..61643761,6	K562	blood:
8	chr10:61627957..61629887-chr10:61630516..61633245,2	MCF-7	breast:
9	chr10:61618470..61621431-chr10:61631382..61633046,2	K562	blood:
10	chr10:61628330..61633371-chr10:61664622..61667776,4	MCF-7	breast:
11	chr10:61628499..61631972-chr10:61632717..61636046,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10509114	0.93[MEX][hapmap];0.81[EUR][1000 genomes]
rs1171787	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1171820	0.89[GIH][hapmap]
rs1171833	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs1180657	0.80[GIH][hapmap]
rs1184089	0.89[GIH][hapmap]
rs12776024	0.85[CHB][hapmap]
rs1624715	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1627130	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1627152	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1628136	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1664254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1664258	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1664260	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1664261	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1664262	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1664263	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1684898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684900	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1684902	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1684903	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1684914	0.85[JPT][hapmap]
rs17202600	0.82[CEU][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17790901	0.87[MEX][hapmap]
rs17791484	0.93[MEX][hapmap]
rs1972950	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2440906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2440908	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2440909	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2440910	0.91[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2440911	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2440918	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2450468	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450469	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2450471	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3763743	0.86[CEU][hapmap]
rs3763745	0.86[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs4146652	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4948249	0.81[CEU][hapmap]
rs61848728	0.82[AMR][1000 genomes]
rs895243	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1664257	SLC16A9	cis	cerebellum	SCAN
rs1664257	CCDC6	cis	cerebellum	SCAN
rs1664257	PHLDB3	trans	cerebellum	SCAN

Chromatin state (count:96 , 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	chr10:61624400-61632000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:61624800-61633000	Weak transcription	Brain Germinal Matrix	brain
7	chr10:61624800-61641000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr10:61625000-61632000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr10:61625000-61632000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr10:61625000-61632600	Weak transcription	Ovary	ovary
11	chr10:61625000-61638800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:61625000-61655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:61625200-61632000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:61625200-61639200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr10:61625800-61632600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr10:61626000-61631800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr10:61626000-61632200	Weak transcription	NHEK	skin
18	chr10:61626000-61632400	Weak transcription	Adipose Nuclei	Adipose
19	chr10:61626400-61632000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr10:61626600-61631800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr10:61627000-61632600	Weak transcription	Brain Substantia Nigra	brain
22	chr10:61628400-61632400	Enhancers	Colon Smooth Muscle	Colon
23	chr10:61628600-61632800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr10:61628600-61632800	Enhancers	K562	blood
25	chr10:61628600-61638600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:61628800-61632000	Weak transcription	Fetal Muscle Leg	muscle
27	chr10:61628800-61632000	Weak transcription	Spleen	Spleen
28	chr10:61628800-61632600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr10:61628800-61632600	Enhancers	Stomach Smooth Muscle	stomach
30	chr10:61629000-61632000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr10:61629000-61632000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr10:61629000-61632400	Weak transcription	Liver	Liver
33	chr10:61629000-61633000	Weak transcription	Hela-S3	cervix
34	chr10:61629000-61634200	Weak transcription	HepG2	liver
35	chr10:61629400-61631800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr10:61629400-61632000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr10:61629600-61632000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr10:61629600-61632600	Weak transcription	Colonic Mucosa	Colon
39	chr10:61629800-61631800	Weak transcription	Fetal Heart	heart
40	chr10:61629800-61632000	Weak transcription	Esophagus	oesophagus
41	chr10:61629800-61632000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr10:61629800-61632000	Weak transcription	Right Atrium	heart
43	chr10:61629800-61632400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr10:61629800-61635400	Enhancers	Brain Hippocampus Middle	brain
45	chr10:61630000-61632000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr10:61630000-61632000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr10:61630000-61647800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:61630200-61631800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr10:61630200-61631800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr10:61630200-61632000	Weak transcription	Right Ventricle	heart

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