Variant report

Variant	rs12090955
Chromosome Location	chr1:67412261-67412262
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67404063..67406127-chr1:67410459..67413110,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10489633	1.00[CHB][hapmap]
rs1074265	1.00[CHB][hapmap]
rs11208980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11208986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11208993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs12059957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12060891	1.00[CHB][hapmap]
rs12069383	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12070382	0.86[ASN][1000 genomes]
rs12073258	1.00[CHB][hapmap]
rs12074407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078209	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12081097	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12082330	0.82[CHB][hapmap]
rs12082503	1.00[CHB][hapmap]
rs12091194	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17097312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17129589	1.00[CHB][hapmap]
rs17129592	1.00[CHB][hapmap]
rs17129595	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17129627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs2985809	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3924795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3924796	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41356950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4553158	1.00[CHB][hapmap]
rs58717164	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6588226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588234	1.00[CHB][hapmap]
rs6681625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6689240	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7517647	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7524757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs7537490	1.00[ASW][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538922	0.85[EUR][1000 genomes]
rs7547791	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7551021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv871720	chr1:67357596-67435161	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12090955	TCTEX1D1	cis	brain	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67396600-67416600	Weak transcription	Spleen	Spleen
2	chr1:67396800-67414400	Weak transcription	Lung	lung
3	chr1:67396800-67429800	Weak transcription	Pancreas	Pancrea
4	chr1:67396800-67458200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:67396800-67459000	Weak transcription	Esophagus	oesophagus
6	chr1:67397600-67413000	Weak transcription	Fetal Brain Female	brain
7	chr1:67397600-67413000	Weak transcription	Fetal Kidney	kidney
8	chr1:67397600-67416600	Weak transcription	Right Ventricle	heart
9	chr1:67397600-67424400	Weak transcription	Colonic Mucosa	Colon
10	chr1:67397600-67457600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:67397800-67412400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:67397800-67412400	Weak transcription	Brain Germinal Matrix	brain
13	chr1:67398400-67414000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:67399000-67416400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:67400400-67413200	Weak transcription	Brain Substantia Nigra	brain
16	chr1:67400400-67413200	Weak transcription	Fetal Lung	lung
17	chr1:67400600-67466600	Weak transcription	Aorta	Aorta
18	chr1:67400800-67413200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:67401200-67413200	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:67403200-67412600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:67403200-67412600	Weak transcription	Psoas Muscle	Psoas
22	chr1:67403200-67419800	Weak transcription	Gastric	stomach
23	chr1:67403200-67429400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:67403400-67412600	Weak transcription	Left Ventricle	heart
25	chr1:67404800-67412400	Weak transcription	Stomach Mucosa	stomach
26	chr1:67405200-67431400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:67405600-67445400	Strong transcription	Fetal Thymus	thymus
28	chr1:67406200-67412600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:67406200-67433000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:67406400-67414000	Strong transcription	Primary B cells from cord blood	blood
31	chr1:67406400-67439200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:67406400-67455600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:67407000-67414400	Weak transcription	Small Intestine	intestine
34	chr1:67407000-67445400	Strong transcription	Dnd41	blood
35	chr1:67407600-67431200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:67408200-67448000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:67408200-67450200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:67408600-67412600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:67409000-67412600	Weak transcription	Primary T cells from cord blood	blood
40	chr1:67409200-67414600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:67409200-67414800	Strong transcription	GM12878-XiMat	blood
42	chr1:67409200-67426400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:67409400-67446400	Weak transcription	Brain Angular Gyrus	brain
44	chr1:67409400-67447600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:67409600-67412400	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:67409600-67413200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:67409600-67419400	Weak transcription	Fetal Heart	heart
48	chr1:67409600-67430400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:67410000-67431200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr1:67410400-67433000	Strong transcription	Duodenum Mucosa	Duodenum

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