Variant report

Variant	rs12164139
Chromosome Location	chr7:27658801-27658802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1009252	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1014373	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1015750	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1030003	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10447552	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10486548	0.82[CHB][hapmap]
rs1052724	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1052741	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10951172	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10951175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10951176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1115346	0.93[ASN][1000 genomes]
rs1115347	0.85[ASN][1000 genomes]
rs11526176	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs11762342	0.93[ASN][1000 genomes]
rs11763449	0.93[ASN][1000 genomes]
rs11764753	0.82[CHB][hapmap]
rs11973492	0.93[ASN][1000 genomes]
rs12155430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12530626	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12531952	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12535844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12537499	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs12540276	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs12665991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12667235	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12667610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12668430	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12670771	1.00[ASN][1000 genomes]
rs12672811	0.93[ASN][1000 genomes]
rs12700813	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12700815	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12700817	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12700822	0.81[ASN][1000 genomes]
rs12700825	0.82[CHB][hapmap]
rs12700826	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12700829	0.82[CHB][hapmap]
rs12700830	0.82[CHB][hapmap]
rs13226102	0.93[ASN][1000 genomes]
rs13227873	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs13237776	1.00[JPT][hapmap]
rs13242248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13244903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13246464	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13308974	0.93[ASN][1000 genomes]
rs1357760	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs1404276	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1404278	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1524526	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1524527	0.88[LWK][hapmap]
rs1524530	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1524531	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1524533	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1608664	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17155546	1.00[JPT][hapmap]
rs1851913	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1880370	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1980329	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1986243	0.84[EUR][1000 genomes]
rs2041714	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs2080245	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2098315	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2110526	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2110528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2160125	0.82[CHB][hapmap]
rs2391445	0.82[CHB][hapmap]
rs2391446	0.82[CHB][hapmap]
rs2391447	0.82[CHB][hapmap]
rs2391449	0.82[ASN][1000 genomes]
rs2391452	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2391453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2391454	0.82[CHB][hapmap]
rs34886410	0.85[EUR][1000 genomes]
rs3823946	0.84[CEU][hapmap]
rs3925338	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs4140899	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs42085	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs42099	1.00[JPT][hapmap]
rs4348389	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4719902	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4722719	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4722724	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4722728	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs56123216	0.87[ASN][1000 genomes]
rs56139857	0.93[ASN][1000 genomes]
rs58747588	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6415251	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6462029	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6462031	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6462034	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6462036	0.83[ASN][1000 genomes]
rs6462037	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6462038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6462039	0.82[CHB][hapmap]
rs6943883	0.82[CHB][hapmap]
rs6944610	0.85[ASN][1000 genomes]
rs6945993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6946075	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6947731	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6948460	0.93[ASN][1000 genomes]
rs6948814	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6954905	0.82[CHB][hapmap]
rs6955074	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6956484	0.82[EUR][1000 genomes]
rs6958747	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6959495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6960834	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6961429	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6963421	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6964190	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6966091	0.82[CHB][hapmap]
rs6966587	0.93[ASN][1000 genomes]
rs6970104	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6974387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6974932	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6975900	0.84[LWK][hapmap];0.82[YRI][hapmap]
rs6980382	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs723699	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs723700	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7455882	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7778320	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7779990	0.82[CHB][hapmap]
rs7783447	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7789788	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7790498	1.00[ASN][1000 genomes]
rs7794292	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7805086	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7806415	0.82[CHB][hapmap]
rs7806812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7811436	0.83[ASN][1000 genomes]
rs961723	0.82[CHB][hapmap]
rs961724	0.82[CHB][hapmap]
rs961725	0.82[CHB][hapmap]
rs9639552	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9639553	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs978447	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs986706	0.82[CHB][hapmap];1.00[JPT][hapmap]

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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv1802647	chr7:27658495-27673924	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12164139	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL
rs12164139	SNX10	cis	cerebellum	SCAN
rs12164139	SCRN1	cis	cerebellum	SCAN
rs12164139	ASAP2	trans	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27646800-27659600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:27647000-27660200	Weak transcription	Small Intestine	intestine
3	chr7:27648600-27659800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:27649200-27659400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:27651600-27659200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:27651800-27674200	Weak transcription	Hela-S3	cervix
7	chr7:27653200-27659400	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:27654400-27696400	Weak transcription	Gastric	stomach
9	chr7:27655200-27660400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:27655400-27665200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:27655600-27659200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:27655600-27660600	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr7:27656400-27659600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:27656400-27659600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:27657000-27660200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr7:27657000-27660400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:27657200-27662200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:27657400-27659000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:27657400-27661800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:27657400-27661800	ZNF genes & repeats	Fetal Intestine Large	intestine
21	chr7:27657400-27662600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr7:27657800-27659000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
23	chr7:27657800-27660000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:27657800-27660000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
25	chr7:27657800-27660200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:27658000-27659800	ZNF genes & repeats	NHDF-Ad	bronchial
27	chr7:27658000-27661400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
28	chr7:27658200-27659000	ZNF genes & repeats	Brain Anterior Caudate	brain
29	chr7:27658200-27661200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:27658200-27661400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
31	chr7:27658400-27659800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
32	chr7:27658400-27660200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
33	chr7:27658400-27660200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:27658400-27660400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
35	chr7:27658400-27661000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:27658400-27661000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:27658400-27661200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
38	chr7:27658400-27661200	ZNF genes & repeats	Fetal Lung	lung
39	chr7:27658400-27661400	ZNF genes & repeats	Liver	Liver
40	chr7:27658400-27662000	ZNF genes & repeats	Dnd41	blood
41	chr7:27658600-27659000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr7:27658600-27660000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
43	chr7:27658600-27661000	ZNF genes & repeats	Brain Substantia Nigra	brain
44	chr7:27658600-27661000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
45	chr7:27658600-27661200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr7:27658600-27661200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
47	chr7:27658800-27659000	ZNF genes & repeats	Ovary	ovary
48	chr7:27658800-27659600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr7:27658800-27659600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr7:27658800-27659600	Weak transcription	Placenta	Placenta

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