Variant report

Variant	rs961724
Chromosome Location	chr7:27658035-27658036
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1005128	0.81[AMR][1000 genomes]
rs10081338	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10081339	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1009252	0.81[AMR][1000 genomes]
rs1014373	0.88[YRI][hapmap]
rs1015265	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1015750	0.81[AMR][1000 genomes]
rs10214930	0.80[CEU][hapmap]
rs10250333	0.80[CEU][hapmap]
rs1030003	0.83[AMR][1000 genomes]
rs10447552	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs10486548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10951173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10951175	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs1115346	0.82[AMR][1000 genomes]
rs1115347	0.82[AMR][1000 genomes]
rs11762342	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11763449	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11764753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11973492	0.84[AMR][1000 genomes]
rs12155430	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs12164139	0.82[CHB][hapmap]
rs12530626	0.82[CHB][hapmap];0.85[AMR][1000 genomes]
rs12531518	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12535844	0.82[CHB][hapmap];0.87[AMR][1000 genomes]
rs12537499	0.81[AMR][1000 genomes]
rs12540063	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12665991	0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12667235	0.82[AMR][1000 genomes]
rs12667610	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12668430	0.83[AMR][1000 genomes]
rs12670771	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12672811	0.88[AMR][1000 genomes]
rs12673949	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12700822	0.83[AMR][1000 genomes]
rs12700823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700824	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12700825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12700826	0.82[CHB][hapmap]
rs12700828	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12700829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12700830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13226102	0.83[AMR][1000 genomes]
rs13242248	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs13244903	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs13246464	0.82[CHB][hapmap];0.87[AMR][1000 genomes]
rs13308974	0.83[AMR][1000 genomes]
rs1404276	0.92[YRI][hapmap]
rs1404278	0.82[AMR][1000 genomes]
rs1404282	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1524529	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1524533	0.81[AMR][1000 genomes]
rs1608663	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1880370	0.90[YRI][hapmap]
rs1980329	0.81[AMR][1000 genomes]
rs1980330	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2041714	0.81[AMR][1000 genomes]
rs2041715	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2110526	0.82[AMR][1000 genomes]
rs2110528	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs2160125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2391444	0.94[CEU][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2391445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2391446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2391447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2391448	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2391449	0.84[AMR][1000 genomes]
rs2391451	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2391452	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs2391453	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs2391454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28416309	0.85[AMR][1000 genomes]
rs28429439	0.81[AMR][1000 genomes]
rs42085	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs42087	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs42088	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs42092	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs42098	0.89[AFR][1000 genomes]
rs4481475	0.80[CEU][hapmap]
rs4719902	0.92[YRI][hapmap]
rs4722724	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4722726	1.00[CEU][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4722728	0.88[AMR][1000 genomes]
rs56139857	0.84[AMR][1000 genomes]
rs6462033	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6462036	0.83[AMR][1000 genomes]
rs6462037	0.81[AMR][1000 genomes]
rs6462038	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6462039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6943883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6945993	0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs6946305	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6947731	0.82[AMR][1000 genomes]
rs6948460	0.88[AMR][1000 genomes]
rs6948814	0.83[AMR][1000 genomes]
rs6954905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6955074	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6957378	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6958747	0.82[CHB][hapmap]
rs6959126	0.81[AMR][1000 genomes]
rs6959495	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs6960834	0.82[AMR][1000 genomes]
rs6963421	0.87[AMR][1000 genomes]
rs6966091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6966587	0.88[AMR][1000 genomes]
rs6970104	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6974387	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6974932	0.82[CHB][hapmap];0.86[AMR][1000 genomes]
rs6980382	0.82[AMR][1000 genomes]
rs759269	0.81[AMR][1000 genomes]
rs759270	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs759271	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7778320	0.82[CHB][hapmap]
rs7779990	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7780431	0.81[AMR][1000 genomes]
rs7782422	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7786973	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7790498	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7794292	0.82[CHB][hapmap]
rs7806415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7806605	0.81[AMR][1000 genomes]
rs7806812	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7808275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7809748	0.82[AMR][1000 genomes]
rs7811436	0.83[AMR][1000 genomes]
rs961723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639552	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs9639559	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs974883	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.85[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs961724	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL
rs961724	HIBADH	Cis_1M	lymphoblastoid	RTeQTL
rs961724	HIBADH	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27628200-27658400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr7:27628600-27658400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:27644400-27658400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr7:27646600-27658400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:27646800-27658800	Weak transcription	Osteobl	bone
6	chr7:27646800-27659600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:27647000-27660200	Weak transcription	Small Intestine	intestine
8	chr7:27648600-27659800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:27648800-27658200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:27648800-27658200	Weak transcription	HSMMtube	muscle
11	chr7:27649000-27658400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:27649200-27659400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:27651200-27658600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:27651400-27658400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:27651600-27659200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:27651800-27674200	Weak transcription	Hela-S3	cervix
17	chr7:27652400-27658600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr7:27652400-27658600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr7:27653200-27659400	Weak transcription	Brain Hippocampus Middle	brain
20	chr7:27654000-27658200	Weak transcription	Brain Anterior Caudate	brain
21	chr7:27654200-27658400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr7:27654400-27658600	Weak transcription	Brain Substantia Nigra	brain
23	chr7:27654400-27658600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr7:27654400-27696400	Weak transcription	Gastric	stomach
25	chr7:27655200-27660400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr7:27655400-27658200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:27655400-27658400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:27655400-27665200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:27655600-27658800	Strong transcription	Primary T cells from cord blood	blood
30	chr7:27655600-27658800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr7:27655600-27658800	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr7:27655600-27659200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:27655600-27660600	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr7:27655800-27658800	Strong transcription	Ovary	ovary
35	chr7:27656200-27658400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:27656200-27658400	Weak transcription	Left Ventricle	heart
37	chr7:27656200-27658600	Weak transcription	Pancreas	Pancrea
38	chr7:27656200-27658600	Weak transcription	Psoas Muscle	Psoas
39	chr7:27656200-27658600	Weak transcription	Thymus	Thymus
40	chr7:27656400-27658200	Weak transcription	Fetal Lung	lung
41	chr7:27656400-27658400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr7:27656400-27658600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:27656400-27659600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr7:27656400-27659600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:27656600-27658400	Genic enhancers	Dnd41	blood
46	chr7:27656800-27658400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr7:27657000-27658800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:27657000-27660200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr7:27657000-27660400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:27657200-27658800	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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