Variant report

Variant	rs1972950
Chromosome Location	chr10:61662065-61662066
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:61628053..61630048-chr10:61661857..61663658,2	K562	blood:
2	chr10:61594610..61596651-chr10:61661878..61664205,2	K562	blood:
3	chr10:61603804..61606777-chr10:61661880..61663736,2	K562	blood:
4	chr10:61661963..61664576-chr10:61749051..61751954,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10509114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs1171833	0.92[CEU][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11817261	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11819256	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1183347	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12572828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12573055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1624715	0.88[CEU][hapmap]
rs1664254	0.85[CEU][hapmap]
rs1664257	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs1664258	0.96[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1664260	0.96[CEU][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs1664262	0.96[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1664276	0.88[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1664278	0.86[EUR][1000 genomes]
rs1664279	0.86[EUR][1000 genomes]
rs1664280	0.86[EUR][1000 genomes]
rs1664281	0.86[EUR][1000 genomes]
rs1684898	0.81[MEX][hapmap];0.82[TSI][hapmap]
rs1684900	0.84[CEU][hapmap]
rs1684902	0.96[CEU][hapmap]
rs1684904	0.86[EUR][1000 genomes]
rs1684916	0.85[EUR][1000 genomes]
rs17201105	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17202345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs17202600	1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap]
rs17790901	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs17791132	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17791436	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17791484	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs17793021	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271561	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2440906	0.96[CEU][hapmap]
rs2440910	0.92[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs2440916	0.86[EUR][1000 genomes]
rs2440918	0.88[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2450462	0.85[EUR][1000 genomes]
rs2450463	0.85[EUR][1000 genomes]
rs2450468	0.96[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs2456712	0.82[CEU][hapmap]
rs3763743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3763745	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3793866	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4948249	1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4948368	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs56221953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61845881	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61845882	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61845883	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61845885	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7478076	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs895243	0.96[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1972950	SLC16A9	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61641600-61664200	Weak transcription	A549	lung
2	chr10:61649800-61664200	Weak transcription	Placenta	Placenta
3	chr10:61650200-61664000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr10:61650200-61664200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr10:61651200-61663400	Enhancers	Colon Smooth Muscle	Colon
6	chr10:61651400-61664000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:61653400-61663800	Enhancers	Fetal Intestine Large	intestine
8	chr10:61654200-61663200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:61654400-61663400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr10:61654800-61663400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:61654800-61663800	Weak transcription	HSMM	muscle
12	chr10:61654800-61664000	Weak transcription	NHLF	lung
13	chr10:61655600-61663800	Weak transcription	Osteobl	bone
14	chr10:61656000-61663800	Weak transcription	NH-A	brain
15	chr10:61656200-61663000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr10:61656200-61664000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr10:61656200-61664200	Weak transcription	Right Ventricle	heart
18	chr10:61656400-61662800	Weak transcription	Brain Substantia Nigra	brain
19	chr10:61656400-61663200	Weak transcription	Brain Angular Gyrus	brain
20	chr10:61657600-61663800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr10:61657600-61664200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr10:61658200-61663200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:61658400-61664000	Weak transcription	Liver	Liver
24	chr10:61658400-61664000	Weak transcription	Right Atrium	heart
25	chr10:61658600-61664200	Weak transcription	Left Ventricle	heart
26	chr10:61658800-61664000	Weak transcription	Fetal Kidney	kidney
27	chr10:61659200-61663400	Weak transcription	Fetal Lung	lung
28	chr10:61659200-61663600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr10:61659200-61663600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:61659400-61664600	Weak transcription	HSMMtube	muscle
31	chr10:61659600-61663400	Weak transcription	Fetal Brain Female	brain
32	chr10:61659800-61663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:61659800-61663600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr10:61659800-61663800	Weak transcription	Fetal Brain Male	brain
35	chr10:61659800-61664000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr10:61659800-61664000	Enhancers	HMEC	breast
37	chr10:61659800-61664000	Weak transcription	HUVEC	blood vessel
38	chr10:61660000-61663800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr10:61660200-61663000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr10:61660200-61663400	Weak transcription	Adipose Nuclei	Adipose
41	chr10:61660400-61662800	Weak transcription	K562	blood
42	chr10:61660400-61663400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr10:61660400-61663400	Weak transcription	Brain Anterior Caudate	brain
44	chr10:61660400-61663400	Active TSS	GM12878-XiMat	blood
45	chr10:61660400-61663600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr10:61660400-61663600	Weak transcription	Fetal Heart	heart
47	chr10:61660400-61663800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr10:61660400-61664000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr10:61660400-61664000	Weak transcription	Fetal Muscle Leg	muscle
50	chr10:61660400-61664000	Weak transcription	Fetal Stomach	stomach

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