Variant report

Variant	rs12700829
Chromosome Location	chr7:27687102-27687103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27685245..27687272-chr7:27689998..27692891,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10081338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10081339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1014373	0.88[YRI][hapmap]
rs1015265	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1030003	0.81[AMR][1000 genomes]
rs10447552	0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10486548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951173	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951175	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1115346	0.80[CEU][hapmap]
rs11762342	0.81[AMR][1000 genomes]
rs11763449	0.81[AMR][1000 genomes]
rs11764753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11973492	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12155430	0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12164139	0.82[CHB][hapmap]
rs12530626	0.82[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes]
rs12531518	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12535844	0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12540063	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665991	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs12667610	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs12668430	0.81[AMR][1000 genomes]
rs12670415	0.82[CEU][hapmap]
rs12670771	0.88[AMR][1000 genomes]
rs12672811	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12673949	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12700822	0.81[AMR][1000 genomes]
rs12700823	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12700824	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700826	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs12700828	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12700830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226102	0.81[AMR][1000 genomes]
rs13242248	0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13244903	0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13246464	0.82[CHB][hapmap];0.90[AMR][1000 genomes]
rs13308974	0.81[AMR][1000 genomes]
rs1404276	0.92[YRI][hapmap]
rs1404282	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1524529	1.00[CEU][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1608663	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1880370	0.90[YRI][hapmap]
rs1980329	0.81[CEU][hapmap]
rs1980330	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2041715	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2110528	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs2160125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391444	0.95[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2391445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2391446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2391447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391448	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391449	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2391451	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391452	0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2391453	0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2391454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28416309	0.82[AMR][1000 genomes]
rs42085	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs42087	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs42088	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs42092	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs42098	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4719902	0.92[YRI][hapmap]
rs4722724	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs4722726	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4722728	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs56139857	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6462031	0.82[CEU][hapmap]
rs6462033	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6462036	0.81[AMR][1000 genomes]
rs6462038	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs6462039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944610	0.82[AMR][1000 genomes]
rs6945993	0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6946305	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948460	0.91[AMR][1000 genomes]
rs6948814	0.81[AMR][1000 genomes]
rs6954905	1.00[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]
rs6957378	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958747	0.82[CHB][hapmap]
rs6959495	0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6963421	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6966091	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]
rs6966587	0.91[AMR][1000 genomes]
rs6970104	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs6974387	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs6974932	0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs759270	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs759271	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7778320	0.82[CHB][hapmap]
rs7779990	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782422	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7786973	1.00[CEU][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7790498	0.88[AMR][1000 genomes]
rs7794292	0.82[CHB][hapmap]
rs7806415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806812	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs7808275	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811436	0.81[AMR][1000 genomes]
rs961723	1.00[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];0.88[ASN][1000 genomes]
rs961724	1.00[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];0.88[ASN][1000 genomes]
rs961725	1.00[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];0.88[ASN][1000 genomes]
rs9639552	1.00[YRI][hapmap]
rs9639559	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs974883	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][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
rs12700829	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL
rs12700829	HIBADH	cis	multi-tissue	Pritchard
rs12700829	HIBADH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27654400-27696400	Weak transcription	Gastric	stomach
2	chr7:27658800-27687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:27658800-27688600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:27660600-27701000	Weak transcription	Right Ventricle	heart
5	chr7:27661000-27688000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:27661200-27694800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr7:27661400-27688800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr7:27661400-27700800	Weak transcription	Thymus	Thymus
9	chr7:27661800-27692200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:27661800-27694400	Weak transcription	Lung	lung
11	chr7:27662600-27688200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr7:27662800-27688000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:27664800-27688200	Weak transcription	K562	blood
14	chr7:27668400-27687400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr7:27671400-27701600	Weak transcription	Spleen	Spleen
16	chr7:27674000-27700800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:27674800-27695200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:27675000-27700800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr7:27675400-27701400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:27676000-27701600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr7:27676200-27693200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr7:27676200-27701600	Weak transcription	Psoas Muscle	Psoas
23	chr7:27676400-27687400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr7:27676600-27700600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr7:27676800-27687200	Weak transcription	Primary B cells from cord blood	blood
26	chr7:27676800-27692000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:27677400-27701400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:27680000-27687200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:27680400-27701000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr7:27680800-27701200	Weak transcription	Small Intestine	intestine
31	chr7:27681000-27701200	Weak transcription	Fetal Muscle Leg	muscle
32	chr7:27681600-27687200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:27681600-27687400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr7:27681600-27687800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:27681600-27691000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr7:27681600-27691200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:27681600-27691600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:27681600-27701400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr7:27681600-27701400	Weak transcription	Fetal Kidney	kidney
40	chr7:27681800-27687200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:27681800-27687200	Weak transcription	Brain Anterior Caudate	brain
42	chr7:27681800-27687200	Weak transcription	Placenta	Placenta
43	chr7:27681800-27687200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:27681800-27688400	Weak transcription	NH-A	brain
45	chr7:27681800-27691400	Weak transcription	Osteobl	bone
46	chr7:27681800-27696600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr7:27681800-27696600	Weak transcription	Brain Substantia Nigra	brain
48	chr7:27681800-27696800	Weak transcription	Brain Hippocampus Middle	brain
49	chr7:27681800-27700400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr7:27681800-27700600	Weak transcription	Colon Smooth Muscle	Colon

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