Variant report

Variant	rs9388873
Chromosome Location	chr6:131317853-131317854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131315063..131319748-chr6:131319876..131324209,7	MCF-7	breast:
2	chr6:131286503..131288563-chr6:131317280..131319051,2	K562	blood:

Variant related genes	Relation type
ENSG00000079819	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10872375	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11154611	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11760051	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195366	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12196734	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12197829	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203760	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs12214021	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1569195	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs17059954	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1976981	0.96[ASN][1000 genomes]
rs2151068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2178282	0.98[ASN][1000 genomes]
rs28812545	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4259270	0.89[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4498389	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs62423583	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6901548	0.96[ASN][1000 genomes]
rs6902930	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6903705	0.98[ASN][1000 genomes]
rs6905151	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6907809	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6916206	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6921542	0.98[ASN][1000 genomes]
rs6926372	0.96[ASN][1000 genomes]
rs7763960	0.96[ASN][1000 genomes]
rs7770892	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9321264	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9372986	0.89[ASN][1000 genomes]
rs9372987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9375784	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9375785	0.80[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375787	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9375788	0.93[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9375789	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9375790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9375794	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9375795	0.91[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9375796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9375797	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs9388876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9388880	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9398967	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9398969	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398970	0.98[ASN][1000 genomes]
rs9398971	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9398972	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398973	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398975	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9398976	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9402301	0.85[ASN][1000 genomes]
rs9402306	0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9402310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9402313	0.98[ASN][1000 genomes]
rs9402314	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9483210	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9492790	0.94[ASN][1000 genomes]
rs9492792	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs951251	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs954919	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[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
rs9388873	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131306800-131320000	Weak transcription	Left Ventricle	heart
2	chr6:131311400-131318400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:131312400-131318400	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:131312600-131321800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:131313000-131318400	Weak transcription	Fetal Kidney	kidney
6	chr6:131314000-131318000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:131314400-131318000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:131314800-131322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:131314800-131325000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:131315200-131321400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:131315400-131318000	Weak transcription	A549	lung
12	chr6:131315400-131318600	Weak transcription	Right Atrium	heart
13	chr6:131315400-131320000	Weak transcription	Right Ventricle	heart
14	chr6:131315600-131318200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:131315600-131321800	Weak transcription	Pancreas	Pancrea
16	chr6:131315800-131318000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:131315800-131318400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:131315800-131318600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:131315800-131320000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:131315800-131321400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:131315800-131321800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:131315800-131321800	Weak transcription	Lung	lung
23	chr6:131315800-131323200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:131315800-131325800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:131316000-131318400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:131316600-131319000	Enhancers	HUVEC	blood vessel
27	chr6:131316800-131318000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:131316800-131318200	Enhancers	NHEK	skin
29	chr6:131316800-131318400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr6:131316800-131318400	Enhancers	Brain Cingulate Gyrus	brain
31	chr6:131316800-131319000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:131316800-131319000	Enhancers	Osteobl	bone
33	chr6:131316800-131319200	Enhancers	Fetal Lung	lung
34	chr6:131316800-131322200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr6:131317000-131318000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:131317000-131318200	Enhancers	Brain Anterior Caudate	brain
37	chr6:131317000-131318400	Enhancers	Brain Hippocampus Middle	brain
38	chr6:131317200-131318600	Enhancers	Brain Substantia Nigra	brain
39	chr6:131317200-131318800	Enhancers	NHLF	lung
40	chr6:131317200-131319000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:131317200-131319000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:131317200-131319000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:131317200-131319000	Enhancers	Adipose Nuclei	Adipose
44	chr6:131317200-131319000	Enhancers	HepG2	liver
45	chr6:131317400-131318200	Enhancers	NH-A	brain
46	chr6:131317400-131318400	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr6:131317400-131318400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr6:131317400-131318400	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:131317400-131318400	Weak transcription	Fetal Heart	heart
50	chr6:131317400-131318600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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