Variant report

Variant	rs12670250
Chromosome Location	chr7:27577103-27577104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10486549	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs12667470	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12671723	0.86[JPT][hapmap]
rs12700831	0.82[JPT][hapmap]
rs13242238	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13245339	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1524525	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1524527	0.91[JPT][hapmap]
rs17155443	0.91[JPT][hapmap]
rs17155498	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17155501	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17155505	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17155525	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17155537	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs17155702	0.82[ASW][hapmap];0.91[CEU][hapmap]
rs2108309	0.88[CEU][hapmap]
rs2192559	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2391450	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2893292	0.91[JPT][hapmap]
rs34905189	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs42089	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs42100	0.90[JPT][hapmap]
rs58231871	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59686784	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61407744	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62454870	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62454871	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62454872	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62456947	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62456951	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6947004	0.85[EUR][1000 genomes]
rs6975900	0.86[JPT][hapmap]
rs72596952	0.84[EUR][1000 genomes]
rs72596966	0.80[EUR][1000 genomes]
rs759268	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs759272	0.86[JPT][hapmap]
rs7778454	0.81[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830930	chr7:27395838-27587355	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12670250	TAX1BP1	cis	cerebellum	SCAN
rs12670250	SCRN1	cis	cerebellum	SCAN
rs12670250	HOXA9	cis	parietal	SCAN
rs12670250	SNX10	cis	cerebellum	SCAN
rs12670250	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL
rs12670250	PRR15	cis	parietal	SCAN
rs12670250	LOC441204	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27553200-27581000	Weak transcription	Fetal Heart	heart
2	chr7:27555800-27581000	Weak transcription	Gastric	stomach
3	chr7:27556000-27579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:27556000-27581600	Weak transcription	HMEC	breast
5	chr7:27556400-27584400	Weak transcription	NHEK	skin
6	chr7:27556400-27586400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:27558000-27579800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:27559400-27584200	Weak transcription	Pancreas	Pancrea
9	chr7:27559400-27627800	Weak transcription	Psoas Muscle	Psoas
10	chr7:27559800-27593000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:27560800-27578800	Weak transcription	NHLF	lung
12	chr7:27561200-27580200	Weak transcription	Colon Smooth Muscle	Colon
13	chr7:27561200-27580600	Strong transcription	Liver	Liver
14	chr7:27561600-27583000	Weak transcription	Colonic Mucosa	Colon
15	chr7:27561800-27580200	Weak transcription	Fetal Stomach	stomach
16	chr7:27562400-27579800	Weak transcription	NH-A	brain
17	chr7:27562400-27581000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:27562400-27581000	Weak transcription	Spleen	Spleen
19	chr7:27563000-27580000	Weak transcription	Fetal Thymus	thymus
20	chr7:27563000-27581000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr7:27563200-27579800	Weak transcription	Brain Angular Gyrus	brain
22	chr7:27563400-27580800	Weak transcription	GM12878-XiMat	blood
23	chr7:27563400-27581800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:27564000-27580800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr7:27564200-27582000	Weak transcription	Stomach Mucosa	stomach
26	chr7:27564200-27585400	Weak transcription	Small Intestine	intestine
27	chr7:27565200-27581600	Weak transcription	Esophagus	oesophagus
28	chr7:27565600-27592200	Weak transcription	Brain Substantia Nigra	brain
29	chr7:27566000-27579800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr7:27566000-27580000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:27566000-27580000	Weak transcription	Thymus	Thymus
32	chr7:27566000-27580200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:27566000-27580600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:27566000-27581000	Weak transcription	Brain Anterior Caudate	brain
35	chr7:27566000-27583800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr7:27566200-27579800	Weak transcription	Hela-S3	cervix
37	chr7:27566200-27580000	Weak transcription	K562	blood
38	chr7:27566400-27579600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr7:27566600-27578200	Weak transcription	Primary B cells from cord blood	blood
40	chr7:27566800-27579800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr7:27566800-27593200	Weak transcription	Lung	lung
42	chr7:27567000-27580000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr7:27567200-27582800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr7:27569000-27579800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr7:27569000-27579800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr7:27569000-27579800	Weak transcription	Osteobl	bone
47	chr7:27569000-27580200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:27569200-27579600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:27569400-27578000	Weak transcription	Brain Hippocampus Middle	brain
50	chr7:27569400-27579200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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