Variant report

Variant	rs2391444
Chromosome Location	chr7:27642420-27642421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27621171..27623544-chr7:27641247..27643936,2	MCF-7	breast:

Extended variants
information (count: 128 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1005128	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10081338	0.84[AMR][1000 genomes]
rs10081339	0.84[AMR][1000 genomes]
rs1009252	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1014373	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1015265	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1015750	0.84[AMR][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]
rs10256159	0.82[YRI][hapmap]
rs1030003	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10486548	0.95[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10499580	0.81[ASN][1000 genomes]
rs10807841	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10951171	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10951172	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10951173	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11764753	0.95[CEU][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11767188	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12531518	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12537499	0.84[AMR][1000 genomes]
rs12540063	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12667235	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12668430	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12670415	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12673949	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700817	0.85[AMR][1000 genomes]
rs12700819	0.85[AMR][1000 genomes]
rs12700822	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12700823	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12700824	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12700825	0.95[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12700828	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12700829	0.95[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12700830	0.95[CEU][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13226102	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13308974	0.86[AMR][1000 genomes]
rs1404276	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1404278	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1404282	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]
rs1524529	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524532	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1524533	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1554641	0.85[AMR][1000 genomes]
rs1608663	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608664	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17136532	0.81[ASN][1000 genomes]
rs17155388	0.81[ASN][1000 genomes]
rs1851913	0.85[AMR][1000 genomes]
rs1880370	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1980329	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1980330	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041714	0.84[AMR][1000 genomes]
rs2041715	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080245	0.82[AMR][1000 genomes]
rs2080246	0.82[AMR][1000 genomes]
rs2098315	0.85[AMR][1000 genomes]
rs2098316	0.82[AMR][1000 genomes]
rs2110526	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2110528	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2160125	0.94[CEU][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2391443	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2391445	0.95[CEU][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2391446	0.94[CEU][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2391447	0.95[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2391448	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2391451	0.95[CEU][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2391454	0.95[CEU][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28416309	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28429439	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3925338	0.85[AMR][1000 genomes]
rs4140899	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs42087	0.95[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs42088	0.89[YRI][hapmap]
rs42092	0.81[AMR][1000 genomes]
rs4348389	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4719900	0.82[AMR][1000 genomes]
rs4719902	1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4722719	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4722726	0.94[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6462029	0.85[AMR][1000 genomes]
rs6462031	0.85[AMR][1000 genomes]
rs6462033	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462034	0.80[AMR][1000 genomes]
rs6462036	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6462037	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6462039	0.95[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6943883	0.95[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6946305	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6947731	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6948814	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6952874	0.81[ASN][1000 genomes]
rs6954905	0.95[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6955074	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6957378	0.95[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6959126	0.84[AMR][1000 genomes]
rs6960834	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6963585	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6966091	0.88[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6974387	1.00[CHB][hapmap]
rs6980308	0.81[ASN][1000 genomes]
rs6980382	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs759269	0.84[AMR][1000 genomes]
rs759270	0.94[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs759271	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7779990	0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7780431	0.84[AMR][1000 genomes]
rs7782422	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7783447	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7786973	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7789788	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7806415	0.94[CEU][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7806605	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7808275	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7811436	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs961723	0.95[CEU][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs961724	0.94[CEU][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs961725	0.95[CEU][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9639552	0.92[YRI][hapmap];0.84[AMR][1000 genomes]
rs9639553	0.85[AMR][1000 genomes]
rs9639559	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639560	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs974883	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]
rs978447	0.85[AMR][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
rs2391444	HIBADH	cis	multi-tissue	Pritchard
rs2391444	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL
rs2391444	HIBADH	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27582400-27650800	Weak transcription	Left Ventricle	heart
2	chr7:27600600-27645600	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:27605800-27645800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:27609400-27651000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:27615600-27657800	Weak transcription	Aorta	Aorta
6	chr7:27616000-27643400	Weak transcription	Fetal Lung	lung
7	chr7:27616000-27650800	Weak transcription	Fetal Kidney	kidney
8	chr7:27618400-27645000	Weak transcription	Fetal Intestine Large	intestine
9	chr7:27619800-27643400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:27625200-27642600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:27625800-27645200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:27626600-27654800	Weak transcription	Placenta	Placenta
13	chr7:27626800-27646200	Weak transcription	Ovary	ovary
14	chr7:27626800-27655800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:27627400-27645800	Weak transcription	HSMM	muscle
16	chr7:27627800-27645000	Weak transcription	NHDF-Ad	bronchial
17	chr7:27628200-27658400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr7:27628600-27658400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr7:27629600-27655400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:27630200-27654600	Weak transcription	Primary B cells from cord blood	blood
21	chr7:27630400-27656800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr7:27631400-27643400	Weak transcription	Hela-S3	cervix
23	chr7:27632200-27655600	Weak transcription	Primary T cells from cord blood	blood
24	chr7:27633000-27645800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:27633400-27645600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:27633400-27645600	Weak transcription	Osteobl	bone
27	chr7:27634200-27645800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr7:27635400-27644400	Weak transcription	Fetal Intestine Small	intestine
29	chr7:27638600-27643400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr7:27638600-27645800	Weak transcription	K562	blood
31	chr7:27639800-27645000	Enhancers	Liver	Liver
32	chr7:27640800-27644400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:27641200-27643400	Weak transcription	HepG2	liver
34	chr7:27641200-27644600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr7:27641400-27642600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:27641600-27644600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:27642000-27642600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr7:27642000-27643000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr7:27642000-27643000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:27642000-27643200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:27642000-27643200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr7:27642200-27642600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr7:27642200-27643000	Active TSS	H1 Cell Line	embryonic stem cell
44	chr7:27642200-27643000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:27642400-27642600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:27642400-27642800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:27642400-27642800	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr7:27642400-27642800	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr7:27642400-27642800	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr7:27642400-27645000	Enhancers	Fetal Brain Male	brain

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