Variant report

Variant	rs9402306
Chromosome Location	chr6:131299847-131299848
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10457561	0.88[CEU][hapmap]
rs10457562	0.81[CEU][hapmap]
rs10457563	0.87[CEU][hapmap]
rs10872375	0.84[ASN][1000 genomes]
rs11154611	0.98[ASN][1000 genomes]
rs11760051	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12193685	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs12195366	0.96[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12196734	0.96[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12197829	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12202345	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs12203760	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12214021	0.85[ASN][1000 genomes]
rs1569195	0.92[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17059954	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs1976981	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2151068	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2178282	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28812545	0.86[ASN][1000 genomes]
rs3777432	0.81[CEU][hapmap]
rs4259270	0.86[ASN][1000 genomes]
rs4498389	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62423583	0.96[ASN][1000 genomes]
rs6901548	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6902930	0.86[ASN][1000 genomes]
rs6903705	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6905151	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6907809	0.83[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs6916206	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6921542	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6926372	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7763960	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7770892	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9321264	0.98[ASN][1000 genomes]
rs9372986	0.91[EUR][1000 genomes]
rs9372987	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9372989	0.91[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs9375776	0.86[JPT][hapmap]
rs9375784	0.95[ASN][1000 genomes]
rs9375785	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9375787	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9375788	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9375789	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9375790	0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9375794	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9375796	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9375797	0.82[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9385567	0.81[CEU][hapmap]
rs9388855	0.86[JPT][hapmap]
rs9388860	0.81[CEU][hapmap]
rs9388873	0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9388876	0.91[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs9398967	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9398969	0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs9398970	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398971	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398972	0.86[ASN][1000 genomes]
rs9398973	0.86[ASN][1000 genomes]
rs9402287	0.86[JPT][hapmap]
rs9402301	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9402310	0.91[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9402313	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9402314	0.85[ASN][1000 genomes]
rs9483210	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9492790	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9492792	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs951251	0.84[ASN][1000 genomes]
rs954919	0.83[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9402306	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131253000-131302200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:131272200-131301000	Weak transcription	Placenta	Placenta
3	chr6:131288200-131306600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:131289600-131300800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:131291800-131306200	Weak transcription	Fetal Intestine Small	intestine
6	chr6:131292400-131306400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:131292800-131302000	Weak transcription	NHLF	lung
8	chr6:131295400-131301400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:131295600-131300000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:131295600-131301400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:131295600-131301400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:131296400-131302200	Weak transcription	HSMM	muscle
13	chr6:131296800-131300000	Weak transcription	HUVEC	blood vessel
14	chr6:131296800-131302600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:131297600-131302800	Enhancers	Brain Cingulate Gyrus	brain
16	chr6:131298000-131300400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr6:131298000-131301600	Enhancers	Brain Substantia Nigra	brain
18	chr6:131298000-131302000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:131298000-131302400	Weak transcription	NHDF-Ad	bronchial
20	chr6:131298200-131300200	Enhancers	Brain Hippocampus Middle	brain
21	chr6:131298400-131300200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:131298400-131300400	Enhancers	Colon Smooth Muscle	Colon
23	chr6:131298400-131300800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:131298600-131300800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:131298800-131314800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:131299000-131306200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:131299000-131309800	Weak transcription	HepG2	liver
28	chr6:131299200-131300400	Enhancers	Ovary	ovary
29	chr6:131299200-131301200	Enhancers	K562	blood
30	chr6:131299200-131304600	Enhancers	Fetal Lung	lung
31	chr6:131299400-131300000	Enhancers	Adipose Nuclei	Adipose
32	chr6:131299400-131300000	Enhancers	Psoas Muscle	Psoas
33	chr6:131299400-131300000	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr6:131299400-131300200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:131299400-131300200	Enhancers	Right Atrium	heart
36	chr6:131299400-131300200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:131299400-131300400	Enhancers	Brain Angular Gyrus	brain
38	chr6:131299400-131300400	Enhancers	Brain Anterior Caudate	brain
39	chr6:131299400-131300400	Enhancers	Spleen	Spleen
40	chr6:131299400-131301000	Weak transcription	Thymus	Thymus
41	chr6:131299400-131301800	Enhancers	Fetal Muscle Leg	muscle
42	chr6:131299400-131303600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:131299600-131300000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:131299600-131300200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr6:131299600-131300400	Enhancers	Fetal Stomach	stomach
46	chr6:131299800-131300000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:131299800-131300200	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr6:131299800-131300200	Enhancers	Fetal Kidney	kidney
49	chr6:131299800-131300200	Enhancers	Rectal Smooth Muscle	rectum
50	chr6:131299800-131300400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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