Variant report

Variant	rs11598546
Chromosome Location	chr10:97915428-97915429
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:97915359-97915730	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97889763..97892237-chr10:97913785..97916695,2	K562	blood:

Variant related genes	Relation type
ZNF518A	TF binding region
ENSG00000177853	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10491070	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10509695	1.00[JPT][hapmap]
rs10509700	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10509701	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10509703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10882718	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs10882723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10882728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11188575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs11188596	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11188604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11188606	0.81[ASN][1000 genomes]
rs11188613	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11188618	0.88[ASN][1000 genomes]
rs11188622	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11188631	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188632	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188635	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[ASN][1000 genomes]
rs11188656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11591374	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs11591959	1.00[JPT][hapmap]
rs11593049	1.00[CHB][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11595809	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11596126	1.00[YRI][hapmap]
rs11597197	0.88[ASN][1000 genomes]
rs11598837	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11599170	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11599662	1.00[YRI][hapmap]
rs12354644	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12359842	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12411569	1.00[JPT][hapmap]
rs12761705	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12768772	1.00[YRI][hapmap]
rs12771933	1.00[YRI][hapmap]
rs12778345	0.82[LWK][hapmap];1.00[YRI][hapmap]
rs17382898	1.00[JPT][hapmap]
rs17383738	0.89[YRI][hapmap]
rs2039616	1.00[CHB][hapmap]
rs2125060	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3961944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs4344425	1.00[JPT][hapmap]
rs60450792	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7081169	0.89[YRI][hapmap]
rs7096164	0.82[LWK][hapmap];1.00[YRI][hapmap]
rs713070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[ASN][1000 genomes]
rs7896077	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7916068	0.94[YRI][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11598546	C10orf12	cis	cerebellum	SCAN
rs11598546	CRTAC1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97890800-97917200	Weak transcription	Small Intestine	intestine
2	chr10:97890800-97922400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:97891000-97927000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:97891400-97916400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr10:97891400-97918200	Weak transcription	NHLF	lung
6	chr10:97891800-97921400	Weak transcription	Stomach Mucosa	stomach
7	chr10:97892400-97924800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:97892800-97924200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr10:97895200-97917600	Weak transcription	NH-A	brain
10	chr10:97897800-97916600	Weak transcription	HMEC	breast
11	chr10:97900400-97916400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr10:97903200-97923000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr10:97903600-97920200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr10:97903800-97916200	Weak transcription	HUVEC	blood vessel
15	chr10:97904000-97918800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:97909000-97918800	Strong transcription	HepG2	liver
17	chr10:97910000-97917800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr10:97910600-97917000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr10:97910600-97918200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr10:97910600-97918400	Strong transcription	Liver	Liver
21	chr10:97910600-97918600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr10:97910600-97918600	Strong transcription	Left Ventricle	heart
23	chr10:97910600-97919200	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:97910600-97919800	Strong transcription	Dnd41	blood
25	chr10:97910800-97917200	Strong transcription	Primary T cells from cord blood	blood
26	chr10:97910800-97918600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:97910800-97918800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr10:97910800-97918800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr10:97910800-97919200	Strong transcription	Fetal Intestine Large	intestine
30	chr10:97910800-97920200	Strong transcription	Fetal Muscle Leg	muscle
31	chr10:97910800-97922200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr10:97911000-97917000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:97911000-97917000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr10:97911000-97917200	Strong transcription	Colon Smooth Muscle	Colon
35	chr10:97911000-97917400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:97911000-97917400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr10:97911000-97917600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr10:97911000-97917600	Strong transcription	Brain Anterior Caudate	brain
39	chr10:97911000-97917600	Strong transcription	Ovary	ovary
40	chr10:97911000-97917800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr10:97911000-97918000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr10:97911000-97918400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:97911000-97918800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:97911000-97919200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr10:97911000-97919400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr10:97911000-97919400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr10:97911000-97919400	Strong transcription	Adipose Nuclei	Adipose
48	chr10:97911000-97919600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr10:97911000-97919600	Strong transcription	Fetal Thymus	thymus
50	chr10:97911000-97919800	Strong transcription	Fetal Lung	lung

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