Variant report

Variant	rs1332492
Chromosome Location	chr6:131351278-131351279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:131345332..131348195-chr6:131348850..131352317,3	MCF-7	breast:
2	chr6:131303458..131306255-chr6:131349749..131352593,2	K562	blood:
3	chr6:131322621..131325440-chr6:131350090..131351837,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10499177	0.91[CHB][hapmap]
rs11154614	0.90[ASN][1000 genomes]
rs11961521	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11969461	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12527232	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12527605	1.00[CHB][hapmap]
rs12528626	0.91[CHB][hapmap]
rs12529894	1.00[CHB][hapmap]
rs12665101	0.88[ASN][1000 genomes]
rs13207929	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13208091	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13209830	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1338906	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17059678	0.83[CHB][hapmap]
rs17059736	0.91[CHB][hapmap]
rs17059852	0.91[CHB][hapmap]
rs17180547	0.89[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977744	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2327006	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs34445705	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34863373	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35273150	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777452	0.91[CHB][hapmap]
rs3798251	0.91[CHB][hapmap]
rs4513821	0.91[CHB][hapmap]
rs66491359	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6908768	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6916434	0.81[ASW][hapmap]
rs6923182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6941909	1.00[CHB][hapmap]
rs72987859	0.98[ASN][1000 genomes]
rs72987891	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72989827	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs72989829	0.90[ASN][1000 genomes]
rs7740558	0.90[AFR][1000 genomes]
rs7743764	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7745206	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9483209	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9492762	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs9492776	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs9492782	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap]
rs9492784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9492785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9492799	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][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
rs1332492	EPB41L2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131345800-131352000	Weak transcription	Lung	lung
2	chr6:131345800-131353200	Weak transcription	Ovary	ovary
3	chr6:131345800-131353800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:131345800-131357600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:131346000-131375000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:131348600-131351600	Enhancers	Adipose Nuclei	Adipose
7	chr6:131348800-131351400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:131349000-131358800	Weak transcription	Pancreas	Pancrea
9	chr6:131349400-131351400	Enhancers	Brain Angular Gyrus	brain
10	chr6:131349600-131351400	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr6:131350000-131351400	Enhancers	Rectal Smooth Muscle	rectum
12	chr6:131350000-131351600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:131350000-131351600	Enhancers	Fetal Heart	heart
14	chr6:131350000-131351600	Enhancers	HSMMtube	muscle
15	chr6:131350000-131351800	Enhancers	A549	lung
16	chr6:131350000-131351800	Enhancers	HepG2	liver
17	chr6:131350000-131353200	Enhancers	Brain Anterior Caudate	brain
18	chr6:131350200-131351600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:131350200-131351600	Enhancers	Brain Hippocampus Middle	brain
20	chr6:131350200-131351800	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:131350200-131352000	Enhancers	HSMM	muscle
22	chr6:131350400-131351400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:131350600-131351600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:131350600-131351600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr6:131350600-131351600	Enhancers	Fetal Lung	lung
26	chr6:131350600-131351600	Enhancers	NHEK	skin
27	chr6:131350600-131351800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:131350600-131351800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr6:131350600-131352000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:131350600-131352000	Enhancers	Brain Cingulate Gyrus	brain
31	chr6:131350800-131351400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr6:131350800-131351400	Enhancers	Duodenum Mucosa	Duodenum
33	chr6:131350800-131351400	Enhancers	Fetal Kidney	kidney
34	chr6:131350800-131351400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr6:131350800-131351400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr6:131350800-131351400	Flanking Active TSS	NH-A	brain
37	chr6:131350800-131351600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr6:131350800-131351600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:131350800-131351600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr6:131350800-131351600	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr6:131350800-131351600	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr6:131350800-131351600	Flanking Active TSS	GM12878-XiMat	blood
43	chr6:131350800-131352000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:131350800-131352000	Enhancers	Fetal Muscle Leg	muscle
45	chr6:131350800-131352200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:131350800-131352200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:131350800-131352200	Enhancers	Brain Substantia Nigra	brain
48	chr6:131351000-131351400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr6:131351000-131351400	Enhancers	Colonic Mucosa	Colon
50	chr6:131351000-131351400	Enhancers	Fetal Intestine Small	intestine

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