Variant report

Variant	rs1664258
Chromosome Location	chr10:61632512-61632513
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	chr10:61631763..61634620-chr10:61659289..61660920,2	MCF-7	breast:
2	chr10:61629487..61632652-chr10:61653201..61655969,3	K562	blood:
3	chr10:61630214..61632918-chr10:61637567..61639312,2	MCF-7	breast:
4	chr10:61631384..61634848-chr10:61664834..61667747,10	MCF-7	breast:
5	chr10:61630078..61632932-chr10:61659731..61661689,2	MCF-7	breast:
6	chr10:61631791..61635794-chr10:61666340..61668454,4	K562	blood:
7	chr10:61627957..61629887-chr10:61630516..61633245,2	MCF-7	breast:
8	chr10:61618470..61621431-chr10:61631382..61633046,2	K562	blood:
9	chr10:61628330..61633371-chr10:61664622..61667776,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10509114	0.87[MEX][hapmap]
rs1171787	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1171820	0.89[GIH][hapmap]
rs1171833	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs1180657	0.80[GIH][hapmap]
rs1184089	0.89[GIH][hapmap]
rs12573055	0.95[CEU][hapmap]
rs12776024	0.85[CHB][hapmap]
rs1624715	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627130	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627152	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628136	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664254	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1664257	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];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664261	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664262	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664263	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1664276	0.84[CEU][hapmap]
rs1684898	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684900	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684903	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684914	0.85[JPT][hapmap]
rs17202345	0.80[EUR][1000 genomes]
rs17202600	0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs17790901	0.81[MEX][hapmap]
rs17791484	0.87[MEX][hapmap]
rs1972950	0.96[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs2440906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440908	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440909	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440910	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440911	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440918	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2450468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450469	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2450471	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763745	0.81[MEX][hapmap]
rs3793866	0.84[CEU][hapmap]
rs4146652	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1664258	SLC16A9	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

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	chr10:61624800-61633000	Weak transcription	Brain Germinal Matrix	brain
6	chr10:61624800-61641000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr10:61625000-61632600	Weak transcription	Ovary	ovary
8	chr10:61625000-61638800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:61625000-61655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:61625200-61639200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr10:61625800-61632600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr10:61627000-61632600	Weak transcription	Brain Substantia Nigra	brain
13	chr10:61628600-61632800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr10:61628600-61632800	Enhancers	K562	blood
15	chr10:61628600-61638600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:61628800-61632600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:61628800-61632600	Enhancers	Stomach Smooth Muscle	stomach
18	chr10:61629000-61633000	Weak transcription	Hela-S3	cervix
19	chr10:61629000-61634200	Weak transcription	HepG2	liver
20	chr10:61629600-61632600	Weak transcription	Colonic Mucosa	Colon
21	chr10:61629800-61635400	Enhancers	Brain Hippocampus Middle	brain
22	chr10:61630000-61647800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr10:61630200-61633400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:61630200-61633400	Enhancers	Fetal Intestine Large	intestine
25	chr10:61630200-61633400	Enhancers	Fetal Stomach	stomach
26	chr10:61630400-61632600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr10:61630400-61633200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr10:61630600-61634000	Enhancers	Fetal Intestine Small	intestine
29	chr10:61630800-61632600	Enhancers	Duodenum Mucosa	Duodenum
30	chr10:61631000-61633400	Enhancers	Psoas Muscle	Psoas
31	chr10:61631000-61635600	Enhancers	H1 Cell Line	embryonic stem cell
32	chr10:61631200-61633200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr10:61631200-61633400	Enhancers	Fetal Thymus	thymus
34	chr10:61631200-61634000	Enhancers	Fetal Lung	lung
35	chr10:61631200-61634400	Enhancers	Stomach Mucosa	stomach
36	chr10:61631200-61635600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr10:61631400-61632600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr10:61631400-61632600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr10:61631400-61632800	Enhancers	Primary B cells from peripheral blood	blood
40	chr10:61631400-61632800	Enhancers	GM12878-XiMat	blood
41	chr10:61631400-61633200	Enhancers	Lung	lung
42	chr10:61631400-61633400	Enhancers	Thymus	Thymus
43	chr10:61631400-61634600	Enhancers	Small Intestine	intestine
44	chr10:61631400-61634800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr10:61631400-61635200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr10:61631400-61635800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr10:61631600-61633200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr10:61631600-61633400	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr10:61631600-61633400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr10:61631600-61634400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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