Variant report

Variant	rs1404282
Chromosome Location	chr7:27585451-27585452
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27575540..27577057-chr7:27584201..27586115,2	K562	blood:

Extended variants
information (count: 152 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1005128	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10081338	0.85[AMR][1000 genomes]
rs10081339	0.85[AMR][1000 genomes]
rs1009252	0.90[AMR][1000 genomes]
rs1014373	1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1015265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1015750	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10224961	0.81[ASN][1000 genomes]
rs10231814	0.88[ASN][1000 genomes]
rs10233212	0.87[ASN][1000 genomes]
rs10240622	0.81[ASN][1000 genomes]
rs10242812	0.81[ASN][1000 genomes]
rs10250333	0.89[MKK][hapmap]
rs10256159	0.88[YRI][hapmap]
rs1030003	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs10447552	1.00[ASW][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs10486548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10499580	0.81[ASN][1000 genomes]
rs1052724	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1052741	0.86[AMR][1000 genomes]
rs10807841	0.91[AMR][1000 genomes]
rs10951171	0.91[AMR][1000 genomes]
rs10951172	0.91[AMR][1000 genomes]
rs10951173	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11764753	1.00[CEU][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11767188	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12530626	0.81[CEU][hapmap]
rs12531518	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12537499	1.00[ASW][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12540063	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12667235	1.00[ASW][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes]
rs12668430	1.00[ASW][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes]
rs12670415	0.81[CEU][hapmap];0.91[AMR][1000 genomes]
rs12673949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700817	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12700819	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12700822	0.87[AMR][1000 genomes]
rs12700823	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12700824	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12700825	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12700826	0.81[CEU][hapmap]
rs12700828	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12700829	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12700830	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13226102	0.87[AMR][1000 genomes]
rs13308974	0.87[AMR][1000 genomes]
rs1404276	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1404278	0.88[AMR][1000 genomes]
rs1524529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524532	0.91[AMR][1000 genomes]
rs1524533	0.90[AMR][1000 genomes]
rs1554641	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1608663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608664	0.91[AMR][1000 genomes]
rs17136532	0.81[ASN][1000 genomes]
rs17155388	0.81[ASN][1000 genomes]
rs1851913	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1880370	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1980329	0.90[AMR][1000 genomes]
rs1980330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037638	0.81[AMR][1000 genomes]
rs2041714	1.00[ASW][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2041715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080245	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2080246	0.88[AMR][1000 genomes]
rs2091171	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2098315	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2098316	0.88[AMR][1000 genomes]
rs2110526	0.86[AMR][1000 genomes]
rs2110528	0.87[AMR][1000 genomes]
rs2160125	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2391443	0.91[AMR][1000 genomes]
rs2391444	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391445	1.00[CEU][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2391446	1.00[CEU][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2391447	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2391448	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2391451	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2391454	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28416309	0.86[AMR][1000 genomes]
rs28429439	0.82[AMR][1000 genomes]
rs3847001	0.86[AMR][1000 genomes]
rs3925338	1.00[ASW][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4140899	1.00[ASW][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes]
rs42085	1.00[ASW][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap]
rs42087	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs42088	0.97[GIH][hapmap];0.80[MEX][hapmap];0.89[YRI][hapmap]
rs42092	0.83[AMR][1000 genomes]
rs4348389	0.91[AMR][1000 genomes]
rs4719898	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4719899	0.82[AMR][1000 genomes]
rs4719900	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4719902	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4722719	1.00[ASW][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes]
rs4722724	0.88[TSI][hapmap]
rs4722726	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4722728	1.00[ASW][hapmap];0.91[TSI][hapmap]
rs6462026	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6462029	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6462031	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6462033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462034	0.86[AMR][1000 genomes]
rs6462036	0.87[AMR][1000 genomes]
rs6462037	0.87[AMR][1000 genomes]
rs6462039	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6943883	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6946305	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6947731	0.88[AMR][1000 genomes]
rs6948814	0.87[AMR][1000 genomes]
rs6949496	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6952874	0.81[ASN][1000 genomes]
rs6954905	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6955074	0.88[AMR][1000 genomes]
rs6957378	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6957674	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6958467	0.82[AMR][1000 genomes]
rs6958747	1.00[ASW][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs6959126	0.90[AMR][1000 genomes]
rs6960834	0.88[AMR][1000 genomes]
rs6963585	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6966091	0.86[CEU][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6970104	0.88[TSI][hapmap]
rs6974052	0.81[AMR][1000 genomes]
rs6974387	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6974932	1.00[ASW][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs6980308	0.81[ASN][1000 genomes]
rs6980382	0.88[AMR][1000 genomes]
rs759269	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs759270	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs759271	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7779990	0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7780431	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7782422	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7783447	0.91[AMR][1000 genomes]
rs7786973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7789788	0.91[AMR][1000 genomes]
rs7796520	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7806415	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7806605	0.90[AMR][1000 genomes]
rs7808275	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7811436	0.87[AMR][1000 genomes]
rs961723	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs961724	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs961725	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9639552	0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9639553	1.00[ASW][hapmap];0.88[LWK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9639559	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639560	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs974883	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]
rs978447	1.00[ASW][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]

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	nsv830930	chr7:27395838-27587355	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1404282	HIBADH	cis	cerebellum	SCAN
rs1404282	HIBADH	cis	lymphoblastoid	seeQTL
rs1404282	HOXA3	cis	parietal	SCAN
rs1404282	HIBADH	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27556400-27586400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:27559400-27627800	Weak transcription	Psoas Muscle	Psoas
3	chr7:27559800-27593000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:27565600-27592200	Weak transcription	Brain Substantia Nigra	brain
5	chr7:27566800-27593200	Weak transcription	Lung	lung
6	chr7:27569600-27602200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:27570000-27586400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:27573400-27590000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:27579000-27596000	Weak transcription	Right Ventricle	heart
10	chr7:27580600-27615000	Weak transcription	Aorta	Aorta
11	chr7:27581200-27588400	Weak transcription	HepG2	liver
12	chr7:27581200-27591400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:27581200-27591600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:27581400-27586000	Weak transcription	HSMMtube	muscle
15	chr7:27581400-27586800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:27581400-27587200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:27581400-27588000	Weak transcription	A549	lung
18	chr7:27581400-27591400	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:27581400-27591600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr7:27581400-27591800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:27581400-27594400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:27581400-27600200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:27581400-27617400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:27581600-27586000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:27581600-27586200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:27581600-27586400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr7:27581600-27586800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:27581600-27587000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:27581600-27587000	Weak transcription	Adipose Nuclei	Adipose
30	chr7:27581600-27594400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:27581600-27600200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr7:27581600-27602800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:27581800-27586400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:27581800-27603000	Weak transcription	Fetal Lung	lung
35	chr7:27582000-27586000	Weak transcription	HSMM	muscle
36	chr7:27582200-27586200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr7:27582200-27603000	Weak transcription	Primary T cells from cord blood	blood
38	chr7:27582400-27585800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr7:27582400-27650800	Weak transcription	Left Ventricle	heart
40	chr7:27582600-27586400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr7:27582600-27587600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:27582600-27589800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:27582600-27591600	Weak transcription	Brain Anterior Caudate	brain
44	chr7:27582800-27586200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:27582800-27586600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:27582800-27586600	Weak transcription	Osteobl	bone
47	chr7:27582800-27591600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:27582800-27592200	Weak transcription	Fetal Stomach	stomach
49	chr7:27582800-27592400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr7:27582800-27592600	Weak transcription	Fetal Muscle Trunk	muscle

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