Variant report

Variant	rs6740092
Chromosome Location	chr2:178210268-178210269
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178208196..178211847-chr2:178255899..178258427,3	K562	blood:
2	chr2:178207678..178210773-chr2:178255899..178258732,5	K562	blood:

Variant related genes	Relation type
ENSG00000018510	Chromatin interaction
ENSG00000213963	Chromatin interaction
ENSG00000116044	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10176724	0.91[CEU][hapmap];0.92[TSI][hapmap]
rs10179975	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10180514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10184488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs10190306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10194452	1.00[CEU][hapmap]
rs10207932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10497504	0.84[CEU][hapmap]
rs10497505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10497506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10497509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.81[ASN][1000 genomes]
rs10754987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10754988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10803911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10803912	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs10930783	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930788	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10930790	1.00[CEU][hapmap]
rs10930793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11681133	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12468046	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs12478545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12621156	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs12693121	1.00[CEU][hapmap]
rs13002088	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13007779	1.00[CEU][hapmap]
rs13017003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13017227	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13392350	1.00[JPT][hapmap]
rs1345138	0.84[CEU][hapmap]
rs1349762	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs1374438	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1453369	1.00[CEU][hapmap]
rs1453374	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1453375	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1530965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1545363	1.00[CEU][hapmap]
rs16865143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16865148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16865187	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16865189	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16865191	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16865322	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16865324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16865337	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17326999	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs17398864	1.00[CEU][hapmap]
rs1867905	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1901823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2084967	1.00[CEU][hapmap]
rs2100395	0.81[ASN][1000 genomes]
rs2123641	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2123643	1.00[CEU][hapmap]
rs2167902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs2167903	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs2178017	0.84[CEU][hapmap]
rs2218575	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2272529	1.00[JPT][hapmap]
rs2293475	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2364733	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2364846	1.00[CEU][hapmap]
rs2364848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap]
rs2364849	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs2364851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs2364852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2886194	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs3754989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs3813260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4130304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4243389	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4350784	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs4402804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.81[ASN][1000 genomes]
rs4585065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4893826	1.00[CEU][hapmap]
rs4893827	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs4893829	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4893930	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4893940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4893942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4893943	0.81[ASN][1000 genomes]
rs4893955	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[TSI][hapmap]
rs4893956	0.84[CEU][hapmap]
rs6414095	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6433664	0.81[ASN][1000 genomes]
rs6433666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6433672	0.84[CEU][hapmap]
rs6433674	1.00[CEU][hapmap]
rs6433676	1.00[CEU][hapmap]
rs6433677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6710109	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs6715365	1.00[CEU][hapmap]
rs6720483	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs6720934	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6721168	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs6724177	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6725331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6732250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs6735504	1.00[CHB][hapmap]
rs6744247	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6744488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6746113	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6754660	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs7570297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7575328	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7578962	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7582179	0.91[CEU][hapmap]
rs7585952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7588049	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7589927	1.00[CEU][hapmap]
rs7594073	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[ASN][1000 genomes]
rs7601132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7602451	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7604299	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs7604668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7608135	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs9288001	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs935426	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs935948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs935949	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv3051	chr2:178193436-178239394	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6740092	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178187600-178216400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:178187800-178210800	Weak transcription	Left Ventricle	heart
3	chr2:178187800-178216400	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:178195200-178213600	Weak transcription	Gastric	stomach
5	chr2:178195400-178211400	Weak transcription	Fetal Intestine Small	intestine
6	chr2:178197200-178211800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:178197200-178211800	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:178197200-178212000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:178197200-178213400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:178197200-178215000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:178197200-178216800	Weak transcription	Primary T cells from cord blood	blood
12	chr2:178197200-178217600	Weak transcription	Primary B cells from cord blood	blood
13	chr2:178197600-178211200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:178197600-178217200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:178197800-178211400	Weak transcription	Fetal Heart	heart
16	chr2:178197800-178214000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:178197800-178215400	Weak transcription	Dnd41	blood
18	chr2:178198000-178210600	Weak transcription	HepG2	liver
19	chr2:178198000-178213000	Weak transcription	Ovary	ovary
20	chr2:178199000-178214400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr2:178199600-178213600	Weak transcription	Brain Angular Gyrus	brain
22	chr2:178200800-178213600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:178201000-178211000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:178201000-178211200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:178202200-178217400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:178203200-178216400	Weak transcription	HSMMtube	muscle
27	chr2:178203200-178217800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:178203400-178210400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:178203400-178215000	Weak transcription	Adipose Nuclei	Adipose
30	chr2:178203400-178216000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:178203400-178216000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:178203400-178217000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:178203400-178244400	Weak transcription	HSMM	muscle
34	chr2:178203600-178213000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:178203800-178214000	Weak transcription	K562	blood
36	chr2:178203800-178221600	Weak transcription	A549	lung
37	chr2:178207000-178210800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:178208800-178214200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:178209600-178211800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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