Variant report

Variant	rs11973492
Chromosome Location	chr7:27680389-27680390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:27675143..27677851-chr7:27679227..27682104,2	MCF-7	breast:
2	chr7:27679604..27681845-chr7:27698642..27701537,2	K562	blood:
3	chr7:27680112..27682122-chr7:27959317..27961173,2	MCF-7	breast:
4	chr7:27679604..27681661-chr7:27699022..27701537,2	K562	blood:
5	chr7:27671208..27672985-chr7:27680349..27682159,2	K562	blood:

Extended variants
information (count: 161 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs1005128	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10081338	0.87[AMR][1000 genomes]
rs10081339	0.87[AMR][1000 genomes]
rs1009252	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1014373	0.84[EUR][1000 genomes]
rs1015750	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1030003	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10447552	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486548	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1052724	0.85[EUR][1000 genomes]
rs1052741	0.83[EUR][1000 genomes]
rs10807841	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10951169	0.81[EUR][1000 genomes]
rs10951171	0.84[EUR][1000 genomes]
rs10951172	0.84[EUR][1000 genomes]
rs10951173	0.84[AMR][1000 genomes]
rs10951175	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951176	1.00[ASN][1000 genomes]
rs1111647	0.81[EUR][1000 genomes]
rs1115346	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1115347	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11762342	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763449	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764753	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11766457	0.80[ASN][1000 genomes]
rs11767188	0.86[EUR][1000 genomes]
rs12111584	0.83[EUR][1000 genomes]
rs12155430	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12164139	0.93[ASN][1000 genomes]
rs12530626	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12531518	0.82[AMR][1000 genomes]
rs12531952	0.87[ASN][1000 genomes]
rs12535844	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537499	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12540063	0.84[AMR][1000 genomes]
rs12665991	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12667235	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12667610	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12668430	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12670415	0.84[EUR][1000 genomes]
rs12670771	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12672811	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700817	0.86[EUR][1000 genomes]
rs12700819	0.85[EUR][1000 genomes]
rs12700822	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12700823	0.84[AMR][1000 genomes]
rs12700824	0.84[AMR][1000 genomes]
rs12700825	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12700828	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12700829	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12700830	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13226102	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13242248	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13244903	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246464	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13308974	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1404276	0.86[EUR][1000 genomes]
rs1404278	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1524526	0.81[ASN][1000 genomes]
rs1524532	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1524533	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1554641	0.86[EUR][1000 genomes]
rs1608664	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1851913	0.85[EUR][1000 genomes]
rs1880370	0.86[EUR][1000 genomes]
rs1980329	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2041714	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2080245	0.85[EUR][1000 genomes]
rs2080246	0.83[EUR][1000 genomes]
rs2091171	0.82[EUR][1000 genomes]
rs2098315	0.84[EUR][1000 genomes]
rs2098316	0.83[EUR][1000 genomes]
rs2110526	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2110528	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2160125	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2391443	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2391447	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2391448	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2391449	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2391451	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2391452	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391453	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391454	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28416309	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28429439	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3847001	0.83[EUR][1000 genomes]
rs3925338	0.86[EUR][1000 genomes]
rs4140899	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs42085	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs42087	0.87[AMR][1000 genomes]
rs42092	0.84[AMR][1000 genomes]
rs42111	0.91[EUR][1000 genomes]
rs4348389	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4719898	0.84[EUR][1000 genomes]
rs4719900	0.85[EUR][1000 genomes]
rs4719902	0.85[EUR][1000 genomes]
rs4722719	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4722724	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4722726	0.86[AMR][1000 genomes]
rs4722728	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56123216	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56139857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58747588	0.93[ASN][1000 genomes]
rs6415251	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6462026	0.84[EUR][1000 genomes]
rs6462029	0.84[EUR][1000 genomes]
rs6462031	0.86[EUR][1000 genomes]
rs6462034	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6462036	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6462037	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6462038	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462039	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6943883	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6944610	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6945993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946305	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6947731	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6948460	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948814	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6949496	0.83[EUR][1000 genomes]
rs6954905	0.84[AMR][1000 genomes]
rs6955074	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6957378	0.87[AMR][1000 genomes]
rs6957674	0.82[EUR][1000 genomes]
rs6959126	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6959495	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960834	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6961429	0.87[ASN][1000 genomes]
rs6963421	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963585	0.86[EUR][1000 genomes]
rs6966091	0.84[AMR][1000 genomes]
rs6966587	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970104	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974052	0.81[EUR][1000 genomes]
rs6974387	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974932	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980382	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs759269	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7778320	0.93[ASN][1000 genomes]
rs7779990	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7780431	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7782422	0.81[AMR][1000 genomes]
rs7783447	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7789788	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7790498	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7794292	0.81[ASN][1000 genomes]
rs7805086	1.00[ASN][1000 genomes]
rs7806415	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7806605	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7806812	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808275	0.84[AMR][1000 genomes]
rs7809748	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7811436	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs961723	0.84[AMR][1000 genomes]
rs961724	0.84[AMR][1000 genomes]
rs961725	0.84[AMR][1000 genomes]
rs9639552	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9639553	0.84[EUR][1000 genomes]
rs9639560	0.84[EUR][1000 genomes]
rs978447	0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11973492	HIBADH	Cis_1M	lymphoblastoid	RTeQTL
rs11973492	HIBADH	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27654400-27696400	Weak transcription	Gastric	stomach
2	chr7:27658800-27687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:27658800-27688600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:27660000-27680600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:27660600-27701000	Weak transcription	Right Ventricle	heart
6	chr7:27661000-27680600	Weak transcription	HepG2	liver
7	chr7:27661000-27688000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr7:27661200-27694800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr7:27661400-27688800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:27661400-27700800	Weak transcription	Thymus	Thymus
11	chr7:27661600-27681000	Weak transcription	NHEK	skin
12	chr7:27661800-27681400	Weak transcription	Pancreas	Pancrea
13	chr7:27661800-27686400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:27661800-27692200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:27661800-27694400	Weak transcription	Lung	lung
16	chr7:27662400-27686800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:27662600-27688200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:27662800-27688000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr7:27664400-27680400	Weak transcription	NH-A	brain
20	chr7:27664600-27681400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:27664800-27688200	Weak transcription	K562	blood
22	chr7:27665000-27680400	Weak transcription	NHDF-Ad	bronchial
23	chr7:27665000-27681000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:27665000-27686000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:27666200-27683200	Weak transcription	Esophagus	oesophagus
26	chr7:27667000-27680800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:27667200-27686000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:27668400-27687400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr7:27668600-27686800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr7:27670400-27681000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:27670400-27686200	Weak transcription	Fetal Stomach	stomach
32	chr7:27671400-27701600	Weak transcription	Spleen	Spleen
33	chr7:27674000-27700800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr7:27674600-27680800	Weak transcription	Left Ventricle	heart
35	chr7:27674800-27686800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:27674800-27695200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:27675000-27680800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr7:27675000-27681000	Weak transcription	Aorta	Aorta
39	chr7:27675000-27700800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr7:27675200-27680600	Weak transcription	Right Atrium	heart
41	chr7:27675400-27680600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr7:27675400-27681200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr7:27675400-27681400	Weak transcription	Brain Substantia Nigra	brain
44	chr7:27675400-27701400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr7:27675600-27685800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr7:27675600-27686600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr7:27675800-27686800	Weak transcription	Dnd41	blood
48	chr7:27676000-27701600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr7:27676200-27680800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr7:27676200-27693200	Weak transcription	Primary monocytes fromperipheralblood	blood

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