Variant report

Variant	rs6966091
Chromosome Location	chr7:27660013-27660014
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1005128	0.81[AMR][1000 genomes]
rs10081338	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10081339	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1009252	0.81[AMR][1000 genomes]
rs1014373	0.86[YRI][hapmap]
rs1015265	0.87[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1015750	0.81[AMR][1000 genomes]
rs1030003	0.83[AMR][1000 genomes]
rs10447552	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs10486548	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951175	0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1115346	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs1115347	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11762342	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11763449	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11764753	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][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];0.99[EUR][1000 genomes];0.89[ASN][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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665991	0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12667235	0.82[AMR][1000 genomes]
rs12667610	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12668430	0.83[AMR][1000 genomes]
rs12670771	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12672811	0.88[AMR][1000 genomes]
rs12673949	0.86[CEU][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12700822	0.83[AMR][1000 genomes]
rs12700823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12700824	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700825	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700826	0.82[CHB][hapmap]
rs12700828	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12700829	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700830	0.87[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];1.00[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	0.89[YRI][hapmap]
rs1404278	0.82[AMR][1000 genomes]
rs1404282	0.86[CEU][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1524529	0.88[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1524533	0.81[AMR][1000 genomes]
rs1608663	0.86[CEU][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1880370	0.89[YRI][hapmap]
rs1980329	0.81[AMR][1000 genomes]
rs1980330	0.88[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2041714	0.81[AMR][1000 genomes]
rs2041715	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2110526	0.82[AMR][1000 genomes]
rs2110528	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs2160125	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391444	0.88[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2391445	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2391446	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2391447	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391448	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391449	0.84[AMR][1000 genomes]
rs2391451	0.88[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391452	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs2391453	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs2391454	0.87[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];1.00[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	0.86[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs42088	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs42092	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs42098	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4719902	0.89[YRI][hapmap]
rs4722724	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4722726	0.87[CEU][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4722728	0.88[AMR][1000 genomes]
rs56139857	0.84[AMR][1000 genomes]
rs6462033	0.88[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6462036	0.83[AMR][1000 genomes]
rs6462037	0.81[AMR][1000 genomes]
rs6462038	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6462039	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943883	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945993	0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs6946305	1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947731	0.82[AMR][1000 genomes]
rs6948460	0.88[AMR][1000 genomes]
rs6948814	0.83[AMR][1000 genomes]
rs6954905	0.88[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]
rs6955074	0.82[AMR][1000 genomes]
rs6957378	0.86[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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]
rs6966587	0.88[AMR][1000 genomes]
rs6970104	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6974387	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[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	0.84[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs759271	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780431	0.81[AMR][1000 genomes]
rs7782422	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7786973	0.88[CEU][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7790498	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7794292	0.82[CHB][hapmap]
rs7806415	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806605	0.81[AMR][1000 genomes]
rs7806812	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7808275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs961724	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]
rs961725	0.88[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]
rs9639552	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs9639559	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs974883	0.87[CEU][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.84[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	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
2	esv1802647	chr7:27658495-27673924	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6966091	HIBADH	Cis_1M	lymphoblastoid	RTeQTL
rs6966091	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL
rs6966091	HIBADH	cis	multi-tissue	Pritchard

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27647000-27660200	Weak transcription	Small Intestine	intestine
2	chr7:27651800-27674200	Weak transcription	Hela-S3	cervix
3	chr7:27654400-27696400	Weak transcription	Gastric	stomach
4	chr7:27655200-27660400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:27655400-27665200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:27655600-27660600	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr7:27657000-27660200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr7:27657000-27660400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:27657200-27662200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:27657400-27661800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:27657400-27661800	ZNF genes & repeats	Fetal Intestine Large	intestine
12	chr7:27657400-27662600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr7:27657800-27660200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:27658000-27661400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
15	chr7:27658200-27661200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:27658200-27661400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
17	chr7:27658400-27660200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
18	chr7:27658400-27660200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:27658400-27660400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
20	chr7:27658400-27661000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:27658400-27661000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:27658400-27661200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr7:27658400-27661200	ZNF genes & repeats	Fetal Lung	lung
24	chr7:27658400-27661400	ZNF genes & repeats	Liver	Liver
25	chr7:27658400-27662000	ZNF genes & repeats	Dnd41	blood
26	chr7:27658600-27661000	ZNF genes & repeats	Brain Substantia Nigra	brain
27	chr7:27658600-27661000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
28	chr7:27658600-27661200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:27658600-27661200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
30	chr7:27658800-27660400	ZNF genes & repeats	Primary T cells from cord blood	blood
31	chr7:27658800-27687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:27658800-27688600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:27659200-27660800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:27659200-27660800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
35	chr7:27659200-27661200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
36	chr7:27659400-27660200	ZNF genes & repeats	Osteobl	bone
37	chr7:27659400-27660400	ZNF genes & repeats	Ovary	ovary
38	chr7:27659400-27661000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:27659400-27661000	ZNF genes & repeats	A549	lung
40	chr7:27659600-27660200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
41	chr7:27659600-27660600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
42	chr7:27659600-27660800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
43	chr7:27659600-27661000	ZNF genes & repeats	HSMM	muscle
44	chr7:27659600-27661400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
45	chr7:27659800-27660400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
46	chr7:27659800-27660400	ZNF genes & repeats	Fetal Kidney	kidney
47	chr7:27659800-27660600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
48	chr7:27659800-27661000	ZNF genes & repeats	HepG2	liver
49	chr7:27659800-27661600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
50	chr7:27659800-27672800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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