Variant report

Variant	rs12141472
Chromosome Location	chr1:85036784-85036785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
2	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:
3	chr1:85035225..85038066-chr1:85038637..85040329,3	MCF-7	breast:
4	chr1:84953201..84955322-chr1:85035250..85039258,3	K562	blood:
5	chr1:85035171..85039138-chr1:85044940..85048929,5	K562	blood:

Variant related genes	Relation type
ENSG00000122432	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000117151	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10493752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164000	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164004	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164005	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119873	0.83[EUR][1000 genomes]
rs12123470	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12127160	0.83[EUR][1000 genomes]
rs12131448	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12137275	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12140532	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143652	0.92[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs12145771	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1517601	0.83[EUR][1000 genomes]
rs1517602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15911	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17374628	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17374941	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1914477	0.83[EUR][1000 genomes]
rs2303307	0.93[CEU][hapmap]
rs2911594	0.88[EUR][1000 genomes]
rs2911598	0.81[CEU][hapmap]
rs2911599	0.87[CEU][hapmap]
rs2945145	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs2945147	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs2994935	0.82[CEU][hapmap]
rs2994948	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4356070	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4907080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517756	0.81[EUR][1000 genomes]

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	nsv1000325	chr1:85032605-85100748	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12141472	CTBS	cis	multi-tissue	Pritchard
rs12141472	SPATA1	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84991000-85038200	Weak transcription	Thymus	Thymus
2	chr1:84992400-85038800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:84998600-85038800	Weak transcription	Right Ventricle	heart
4	chr1:85002000-85038400	Weak transcription	Aorta	Aorta
5	chr1:85006600-85038600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:85007200-85038600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:85008800-85039000	Weak transcription	Fetal Brain Male	brain
8	chr1:85009400-85037000	Weak transcription	HUVEC	blood vessel
9	chr1:85014800-85039600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:85017400-85039600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:85019200-85038400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:85022000-85038800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:85024800-85038800	Weak transcription	Brain Angular Gyrus	brain
14	chr1:85025400-85037000	Weak transcription	Small Intestine	intestine
15	chr1:85025600-85038800	Weak transcription	HSMMtube	muscle
16	chr1:85025800-85038800	Weak transcription	Brain Substantia Nigra	brain
17	chr1:85025800-85038800	Weak transcription	Fetal Heart	heart
18	chr1:85026200-85038800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:85027200-85037000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:85027200-85038600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:85027400-85037600	Weak transcription	HepG2	liver
22	chr1:85027800-85038600	Weak transcription	Fetal Kidney	kidney
23	chr1:85028000-85038600	Weak transcription	Fetal Lung	lung
24	chr1:85028200-85037000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:85028200-85038800	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:85028200-85038800	Weak transcription	HSMM	muscle
27	chr1:85028800-85039600	Weak transcription	Gastric	stomach
28	chr1:85029000-85037400	Weak transcription	Dnd41	blood
29	chr1:85029000-85038800	Weak transcription	A549	lung
30	chr1:85029200-85038600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:85029600-85038600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:85030800-85038800	Weak transcription	Fetal Stomach	stomach
33	chr1:85031000-85037400	Weak transcription	Fetal Intestine Small	intestine
34	chr1:85031000-85038200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:85031200-85038600	Weak transcription	Brain Anterior Caudate	brain
36	chr1:85032200-85037000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:85032200-85038600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:85032800-85038600	Weak transcription	Psoas Muscle	Psoas
39	chr1:85033200-85036800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:85033200-85037000	Strong transcription	Primary T cells from cord blood	blood
41	chr1:85033600-85036800	Strong transcription	Primary B cells from cord blood	blood
42	chr1:85033600-85036800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:85033600-85037400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:85033800-85037200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:85034000-85038800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:85034200-85037400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:85034600-85039400	Weak transcription	Esophagus	oesophagus
48	chr1:85035200-85038400	Weak transcription	Spleen	Spleen
49	chr1:85035400-85036800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:85035400-85037200	Weak transcription	Duodenum Mucosa	Duodenum

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