Variant report

Variant	rs17202600
Chromosome Location	chr10:61626372-61626373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:61623680..61630815-chr10:61664299..61668134,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10509114	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10994058	0.81[CEU][hapmap]
rs1171787	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12573055	1.00[CHB][hapmap]
rs1627130	0.81[AMR][1000 genomes]
rs1627152	0.81[AMR][1000 genomes]
rs1628136	0.81[AMR][1000 genomes]
rs1664254	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1664257	0.82[CEU][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1664258	0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs1664260	0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs1664261	0.81[AMR][1000 genomes]
rs1664262	0.87[MEX][hapmap];0.81[AMR][1000 genomes]
rs1664263	0.81[AMR][1000 genomes]
rs1684898	0.87[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1684902	0.81[AMR][1000 genomes]
rs17201105	0.87[CEU][hapmap];0.85[CHB][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17202345	1.00[CHB][hapmap];0.90[GIH][hapmap];0.89[ASN][1000 genomes]
rs17790901	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[MEX][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17791132	0.91[CEU][hapmap];0.85[CHB][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17791436	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs17791484	0.85[CHB][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs1822913	0.81[MEX][hapmap]
rs1972950	1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap]
rs2271561	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs2440906	0.81[AMR][1000 genomes]
rs2440908	0.81[AMR][1000 genomes]
rs2440910	0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs2440911	0.82[AMR][1000 genomes]
rs2450468	0.87[MEX][hapmap];0.81[AMR][1000 genomes]
rs2450469	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2450471	0.82[AMR][1000 genomes]
rs3763743	1.00[CHB][hapmap]
rs3763745	1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap]
rs3793866	1.00[CHB][hapmap]
rs4146652	0.81[AMR][1000 genomes]
rs4948368	0.85[CHB][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs4948369	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55826266	0.84[ASN][1000 genomes]
rs55909789	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61848700	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61848703	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61848704	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61848705	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61848728	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895243	0.87[MEX][hapmap];0.81[AMR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17202600	SLC16A9	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61571400-61628000	Weak transcription	Spleen	Spleen
2	chr10:61583200-61640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:61593200-61629400	Weak transcription	Lung	lung
4	chr10:61608000-61637200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:61610400-61628000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr10:61614200-61629400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr10:61615200-61628000	Weak transcription	Esophagus	oesophagus
8	chr10:61616600-61626600	Weak transcription	Aorta	Aorta
9	chr10:61618000-61632600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr10:61618400-61628600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:61618600-61633200	Weak transcription	HSMM	muscle
12	chr10:61621200-61628400	Weak transcription	Fetal Intestine Large	intestine
13	chr10:61621200-61630200	Weak transcription	Fetal Stomach	stomach
14	chr10:61621800-61628400	Weak transcription	Fetal Muscle Leg	muscle
15	chr10:61623800-61626800	Enhancers	Colon Smooth Muscle	Colon
16	chr10:61623800-61628000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr10:61624000-61626600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr10:61624000-61626800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr10:61624200-61626400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr10:61624200-61626600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr10:61624200-61627000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr10:61624200-61627000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr10:61624200-61627200	Enhancers	Primary B cells from peripheral blood	blood
24	chr10:61624200-61627400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr10:61624200-61630400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr10:61624400-61626800	Enhancers	Primary T cells fromperipheralblood	blood
27	chr10:61624400-61627000	Enhancers	Brain Substantia Nigra	brain
28	chr10:61624400-61630400	Enhancers	Pancreas	Pancrea
29	chr10:61624400-61632000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr10:61624600-61631200	Weak transcription	Fetal Lung	lung
31	chr10:61624800-61626400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr10:61624800-61626400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:61624800-61628600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr10:61624800-61633000	Weak transcription	Brain Germinal Matrix	brain
35	chr10:61624800-61641000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr10:61625000-61626800	Enhancers	Primary T cells from cord blood	blood
37	chr10:61625000-61626800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr10:61625000-61627400	Weak transcription	Colonic Mucosa	Colon
39	chr10:61625000-61627800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr10:61625000-61627800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr10:61625000-61628200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr10:61625000-61628200	Weak transcription	Hela-S3	cervix
43	chr10:61625000-61628400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr10:61625000-61628800	Weak transcription	Right Ventricle	heart
45	chr10:61625000-61628800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr10:61625000-61629400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr10:61625000-61629400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr10:61625000-61629400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr10:61625000-61632000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr10:61625000-61632000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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