Variant report

Variant	rs9390092
Chromosome Location	chr6:143761582-143761583
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143761031..143767695-chr6:143768053..143772068,9	MCF-7	breast:
2	chr6:143760601..143762958-chr6:143820757..143822738,2	K562	blood:

Variant related genes	Relation type
ENSG00000189007	Chromatin interaction
ENSG00000034693	Chromatin interaction
ENSG00000223203	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1061220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1065355	0.84[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs10809	0.80[JPT][hapmap]
rs1111355	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12196227	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1424922	0.81[JPT][hapmap]
rs2143137	0.81[JPT][hapmap]
rs2272924	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2294505	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs2294506	0.81[JPT][hapmap]
rs2496590	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2496593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3088203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761999	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762001	0.81[JPT][hapmap]
rs3762002	0.81[JPT][hapmap]
rs3789790	0.81[JPT][hapmap]
rs3804538	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs3804539	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs3804544	0.87[JPT][hapmap]
rs4895612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4895614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4895615	0.81[JPT][hapmap]
rs4896656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4896660	0.81[JPT][hapmap]
rs6926733	0.81[JPT][hapmap]
rs6929191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6935346	0.81[JPT][hapmap]
rs6935618	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7741976	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7746655	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9321913	0.84[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs9373391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373393	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs9376750	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9376753	0.81[JPT][hapmap]
rs9390090	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390094	0.81[JPT][hapmap]
rs9403494	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs9403496	0.81[CHD][hapmap];0.81[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9390092	KIAA1530	trans	cerebellum	SCAN
rs9390092	ADAT2	cis	parietal	SCAN
rs9390092	ADAT2	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143726800-143765000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:143733200-143770400	Weak transcription	A549	lung
3	chr6:143742400-143770800	Weak transcription	Spleen	Spleen
4	chr6:143742800-143770200	Weak transcription	Psoas Muscle	Psoas
5	chr6:143744400-143770800	Weak transcription	Left Ventricle	heart
6	chr6:143745800-143770600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:143747400-143762800	Strong transcription	K562	blood
8	chr6:143747400-143770600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:143748000-143770400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr6:143748200-143770600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:143748400-143762600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:143748400-143762600	Weak transcription	Osteobl	bone
13	chr6:143748400-143770400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:143748400-143770600	Weak transcription	Fetal Kidney	kidney
15	chr6:143748400-143770600	Weak transcription	NHDF-Ad	bronchial
16	chr6:143748400-143770600	Weak transcription	NHLF	lung
17	chr6:143749400-143762800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:143749400-143770400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:143749600-143770800	Weak transcription	Esophagus	oesophagus
20	chr6:143749800-143770400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:143750800-143762800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:143750800-143770200	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:143750800-143770200	Weak transcription	Thymus	Thymus
24	chr6:143751000-143770800	Weak transcription	HSMMtube	muscle
25	chr6:143751600-143770200	Weak transcription	Fetal Intestine Small	intestine
26	chr6:143751600-143770400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:143751600-143770800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:143752000-143763000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:143752200-143762800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:143752200-143765000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:143752200-143765000	Weak transcription	Small Intestine	intestine
32	chr6:143752400-143770200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:143752600-143762600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:143752600-143766400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:143752600-143770600	Weak transcription	Brain Substantia Nigra	brain
36	chr6:143753000-143770200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:143753800-143762600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:143753800-143770400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:143754000-143765000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:143754000-143770200	Weak transcription	Hela-S3	cervix
41	chr6:143754200-143770400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr6:143755200-143770800	Weak transcription	Gastric	stomach
43	chr6:143755200-143770800	Weak transcription	Ovary	ovary
44	chr6:143755400-143770400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:143756000-143770600	Weak transcription	Fetal Brain Female	brain
46	chr6:143757000-143761800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:143757200-143764200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr6:143757400-143762400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr6:143757600-143762000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:143757600-143770200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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