Variant report

Variant	rs6415251
Chromosome Location	chr7:27668698-27668699
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:27667898..27670542-chr7:27670905..27674481,3	MCF-7	breast:
2	chr7:27668160..27670019-chr7:27701682..27704440,2	K562	blood:
3	chr7:27668160..27670607-chr7:27701639..27704440,2	K562	blood:

Variant related genes	Relation type
ENSG00000106049	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1005128	0.81[EUR][1000 genomes]
rs1009252	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1014373	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1015750	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1030003	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10447552	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1052724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1052741	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10807841	0.81[EUR][1000 genomes]
rs10951171	0.81[EUR][1000 genomes]
rs10951172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10951175	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10951176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1115346	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1115347	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11526176	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11762342	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11763449	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11767188	0.83[EUR][1000 genomes]
rs11973492	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12155430	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12164139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12530626	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12535844	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12537499	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12540276	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12665991	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12667235	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12667610	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12668430	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12670415	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs12670771	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12672811	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12700813	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12700815	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12700817	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12700819	0.82[EUR][1000 genomes]
rs12700822	0.84[EUR][1000 genomes]
rs12700826	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13226102	0.83[EUR][1000 genomes]
rs13227873	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13237776	1.00[JPT][hapmap]
rs13242248	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13244903	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13246464	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13308974	0.83[EUR][1000 genomes]
rs1357760	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1404276	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1404278	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1524530	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1524531	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1524532	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1524533	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1554641	0.83[EUR][1000 genomes]
rs1608664	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17155546	1.00[JPT][hapmap]
rs1851913	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1880370	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1980329	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2041714	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2080245	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2098315	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2110526	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2110528	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2391443	0.81[EUR][1000 genomes]
rs2391449	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391452	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2391453	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28416309	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28429439	0.83[EUR][1000 genomes]
rs3925338	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4140899	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs42085	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs42099	1.00[JPT][hapmap]
rs42111	0.85[EUR][1000 genomes]
rs4348389	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4719898	0.81[EUR][1000 genomes]
rs4719900	0.81[EUR][1000 genomes]
rs4719902	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4722719	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4722724	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4722728	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56139857	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6462026	0.81[EUR][1000 genomes]
rs6462029	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6462031	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6462034	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6462036	0.84[EUR][1000 genomes]
rs6462037	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6462038	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6944610	0.90[EUR][1000 genomes]
rs6945993	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6946075	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6947731	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6948460	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6948814	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6955074	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6958747	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6959495	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6960834	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6961429	1.00[JPT][hapmap]
rs6963421	0.89[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6963585	0.83[EUR][1000 genomes]
rs6964190	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6966587	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6970104	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6974387	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6974932	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6980382	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs723699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs723700	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7455882	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs759269	0.83[EUR][1000 genomes]
rs7778320	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7780431	0.83[EUR][1000 genomes]
rs7783447	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7789788	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7790498	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7794292	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7805086	0.83[ASN][1000 genomes]
rs7806605	0.81[EUR][1000 genomes]
rs7806812	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7809748	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7811436	0.84[EUR][1000 genomes]
rs9639552	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9639553	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9639560	0.81[EUR][1000 genomes]
rs978447	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs986706	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6415251	HIBADH	Cis_1M	lymphoblastoid	RTeQTL
rs6415251	HIBADH	cis	multi-tissue	Pritchard

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27651800-27674200	Weak transcription	Hela-S3	cervix
2	chr7:27654400-27696400	Weak transcription	Gastric	stomach
3	chr7:27658800-27687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:27658800-27688600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:27659800-27672800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:27659800-27675400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr7:27659800-27679000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:27660000-27669800	Weak transcription	Left Ventricle	heart
9	chr7:27660000-27680600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:27660200-27674600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:27660400-27675600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:27660400-27680200	Weak transcription	Fetal Kidney	kidney
13	chr7:27660600-27674800	Weak transcription	Psoas Muscle	Psoas
14	chr7:27660600-27701000	Weak transcription	Right Ventricle	heart
15	chr7:27660800-27675600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:27660800-27676400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:27661000-27675000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr7:27661000-27675400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:27661000-27679600	Weak transcription	HSMMtube	muscle
20	chr7:27661000-27680600	Weak transcription	HepG2	liver
21	chr7:27661000-27688000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr7:27661200-27675200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr7:27661200-27694800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr7:27661400-27669800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:27661400-27670000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr7:27661400-27675200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr7:27661400-27688800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr7:27661400-27700800	Weak transcription	Thymus	Thymus
29	chr7:27661600-27681000	Weak transcription	NHEK	skin
30	chr7:27661800-27669800	Weak transcription	Fetal Stomach	stomach
31	chr7:27661800-27674400	Weak transcription	Aorta	Aorta
32	chr7:27661800-27675800	Weak transcription	Primary B cells from cord blood	blood
33	chr7:27661800-27680200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr7:27661800-27681400	Weak transcription	Pancreas	Pancrea
35	chr7:27661800-27686400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:27661800-27692200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:27661800-27694400	Weak transcription	Lung	lung
38	chr7:27662000-27675200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:27662200-27674400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr7:27662400-27686800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr7:27662600-27688200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:27662800-27674200	Weak transcription	Brain Substantia Nigra	brain
43	chr7:27662800-27688000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr7:27663000-27670800	Weak transcription	Primary T cells from cord blood	blood
45	chr7:27663000-27674400	Weak transcription	Brain Angular Gyrus	brain
46	chr7:27663200-27674400	Weak transcription	Brain Hippocampus Middle	brain
47	chr7:27663200-27675000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr7:27663800-27669800	Weak transcription	Fetal Intestine Small	intestine
49	chr7:27664000-27675200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr7:27664400-27680400	Weak transcription	NH-A	brain

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