Variant report

Variant	rs1554641
Chromosome Location	chr7:27594687-27594688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 159 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1005128	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1009252	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1014373	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1015265	0.88[AMR][1000 genomes]
rs1015750	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1030003	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10447552	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1052724	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052741	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807841	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951169	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951171	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951172	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951175	0.87[EUR][1000 genomes]
rs1111647	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1115346	0.82[EUR][1000 genomes]
rs1115347	0.84[EUR][1000 genomes]
rs11526176	1.00[ASN][1000 genomes]
rs11762342	0.85[EUR][1000 genomes]
rs11763449	0.85[EUR][1000 genomes]
rs11767188	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973492	0.86[EUR][1000 genomes]
rs12155430	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12530626	0.82[EUR][1000 genomes]
rs12535844	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12537499	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539707	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12540276	1.00[ASN][1000 genomes]
rs12665991	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12667235	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12667610	0.85[EUR][1000 genomes]
rs12668430	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670415	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12670771	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12672811	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12673949	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12700813	1.00[ASN][1000 genomes]
rs12700815	1.00[ASN][1000 genomes]
rs12700817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12700822	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13226102	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13227873	1.00[ASN][1000 genomes]
rs13242248	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13244903	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13246464	0.82[AMR][1000 genomes]
rs13308974	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1357760	1.00[ASN][1000 genomes]
rs1404276	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404278	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404282	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1524526	0.90[ASN][1000 genomes]
rs1524529	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1524530	1.00[ASN][1000 genomes]
rs1524531	1.00[ASN][1000 genomes]
rs1524532	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524533	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608663	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1608664	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851911	0.90[ASN][1000 genomes]
rs1851912	0.90[ASN][1000 genomes]
rs1851913	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880370	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980329	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980330	0.91[AMR][1000 genomes]
rs1986243	1.00[ASN][1000 genomes]
rs2037638	0.89[AMR][1000 genomes]
rs2041714	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041715	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2080245	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080246	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091171	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098315	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098316	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110526	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110528	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391443	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391444	0.85[AMR][1000 genomes]
rs2391445	0.87[AMR][1000 genomes]
rs2391446	0.87[AMR][1000 genomes]
rs2391449	0.84[EUR][1000 genomes]
rs2391452	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2391453	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28416309	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28429439	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34886410	1.00[ASN][1000 genomes]
rs3847001	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3925338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4140899	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42085	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4348389	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719898	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719899	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4719900	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719902	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722719	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722724	0.86[EUR][1000 genomes]
rs4722728	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56024263	0.82[EUR][1000 genomes]
rs56139857	0.86[EUR][1000 genomes]
rs6415251	0.83[EUR][1000 genomes]
rs6462026	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462029	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462032	1.00[ASN][1000 genomes]
rs6462033	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6462034	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6462036	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462037	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462038	0.85[EUR][1000 genomes]
rs6944610	0.80[EUR][1000 genomes]
rs6945993	0.86[EUR][1000 genomes]
rs6946075	1.00[ASN][1000 genomes]
rs6947731	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948460	0.84[AMR][1000 genomes]
rs6948814	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949496	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955074	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956484	1.00[ASN][1000 genomes]
rs6957674	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958467	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6959126	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6959495	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6960834	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963421	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6963585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964190	1.00[ASN][1000 genomes]
rs6966587	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6966918	1.00[ASN][1000 genomes]
rs6970104	0.85[EUR][1000 genomes]
rs6974052	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974387	0.85[EUR][1000 genomes]
rs6974932	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6980382	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723699	1.00[ASN][1000 genomes]
rs723700	1.00[ASN][1000 genomes]
rs7455882	1.00[ASN][1000 genomes]
rs759269	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759270	0.87[AMR][1000 genomes]
rs759271	0.87[AMR][1000 genomes]
rs7779240	1.00[ASN][1000 genomes]
rs7780431	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783447	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7786973	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7789788	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790498	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7794292	0.90[ASN][1000 genomes]
rs7806605	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806812	0.85[EUR][1000 genomes]
rs7811436	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs940525	1.00[ASN][1000 genomes]
rs940526	1.00[ASN][1000 genomes]
rs9639552	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639553	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639559	0.91[AMR][1000 genomes]
rs9639560	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974883	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs978447	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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
rs1554641	HIBADH	Cis_1M	lymphoblastoid	RTeQTL
rs1554641	HIBADH	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27559400-27627800	Weak transcription	Psoas Muscle	Psoas
2	chr7:27569600-27602200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:27579000-27596000	Weak transcription	Right Ventricle	heart
4	chr7:27580600-27615000	Weak transcription	Aorta	Aorta
5	chr7:27581400-27600200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:27581400-27617400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:27581600-27600200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:27581600-27602800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:27581800-27603000	Weak transcription	Fetal Lung	lung
10	chr7:27582200-27603000	Weak transcription	Primary T cells from cord blood	blood
11	chr7:27582400-27650800	Weak transcription	Left Ventricle	heart
12	chr7:27582800-27595400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:27582800-27600200	Weak transcription	NHDF-Ad	bronchial
14	chr7:27582800-27604800	Weak transcription	Fetal Kidney	kidney
15	chr7:27582800-27615000	Weak transcription	Placenta	Placenta
16	chr7:27582800-27615200	Weak transcription	Ovary	ovary
17	chr7:27583200-27598800	Weak transcription	Fetal Intestine Large	intestine
18	chr7:27587400-27602600	Weak transcription	Adipose Nuclei	Adipose
19	chr7:27587800-27600200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:27587800-27602600	Weak transcription	HSMM	muscle
21	chr7:27588600-27594800	Weak transcription	A549	lung
22	chr7:27588600-27596400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:27593200-27600400	Weak transcription	Liver	Liver
24	chr7:27593400-27597600	Weak transcription	Brain Hippocampus Middle	brain
25	chr7:27594200-27595400	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr7:27594200-27595600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr7:27594200-27595600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr7:27594200-27595800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr7:27594400-27594800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr7:27594400-27595200	Enhancers	H1 Cell Line	embryonic stem cell
31	chr7:27594400-27595200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:27594400-27595200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr7:27594400-27595400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr7:27594400-27595600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr7:27594400-27595600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr7:27594400-27596000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:27594600-27595800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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