Variant report

Variant	rs11969461
Chromosome Location	chr6:131339257-131339258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:131339160-131339310	GM12872	blood:	n/a	n/a
2	KAP1	chr6:131339188-131339421	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10499177	0.91[CHB][hapmap]
rs11154614	0.90[ASN][1000 genomes]
rs11961521	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12527232	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12527605	0.91[CHB][hapmap]
rs12528626	0.91[CHB][hapmap]
rs12529894	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs12663183	0.82[CHB][hapmap]
rs12665101	0.88[ASN][1000 genomes]
rs13207929	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13208091	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13209830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1332492	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]
rs1338906	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17059678	0.82[CHB][hapmap]
rs17059736	0.91[CHB][hapmap]
rs17059852	0.91[CHB][hapmap]
rs17180547	1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1855078	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]
rs1977744	0.92[ASN][1000 genomes]
rs2327006	0.93[CEU][hapmap];0.91[CHB][hapmap]
rs2327007	0.80[ASN][1000 genomes]
rs34445705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34863373	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35273150	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777452	0.91[CHB][hapmap]
rs3798251	0.91[CHB][hapmap]
rs4513821	0.91[CHB][hapmap]
rs66491359	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6908768	0.92[ASN][1000 genomes]
rs6923182	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6941909	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs72987859	0.98[ASN][1000 genomes]
rs72987891	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72989827	0.90[ASN][1000 genomes]
rs72989829	0.90[ASN][1000 genomes]
rs7743764	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7745206	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs946349	0.80[ASN][1000 genomes]
rs9483209	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9492762	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs9492776	0.93[CEU][hapmap];0.91[CHB][hapmap]
rs9492782	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9492784	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9492785	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9492799	0.88[AMR][1000 genomes];0.84[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
rs11969461	EPB41L2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131329800-131347400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:131332200-131345400	Weak transcription	Left Ventricle	heart
3	chr6:131332800-131339600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:131334800-131342800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:131335200-131343200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:131335600-131345200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:131336600-131345200	Weak transcription	Ovary	ovary
8	chr6:131337200-131345000	Weak transcription	Hela-S3	cervix
9	chr6:131337200-131345000	Weak transcription	NHLF	lung
10	chr6:131337400-131339600	Weak transcription	HMEC	breast
11	chr6:131337400-131347200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:131337600-131345200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:131337800-131345000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:131337800-131345000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:131337800-131345200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:131337800-131345400	Weak transcription	Right Atrium	heart
17	chr6:131337800-131351000	Weak transcription	Stomach Mucosa	stomach
18	chr6:131338000-131339400	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:131338000-131339600	Enhancers	A549	lung
20	chr6:131338000-131345000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:131338000-131345000	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:131338000-131345000	Weak transcription	NHDF-Ad	bronchial
23	chr6:131338000-131345200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:131338200-131345200	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:131338200-131345200	Weak transcription	HepG2	liver
26	chr6:131338800-131339400	Enhancers	Brain Anterior Caudate	brain
27	chr6:131338800-131340200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:131339000-131339400	Enhancers	Brain Angular Gyrus	brain
29	chr6:131339200-131339600	Enhancers	Brain Substantia Nigra	brain
30	chr6:131339200-131339600	Enhancers	Gastric	stomach
31	chr6:131339200-131339600	Enhancers	Pancreas	Pancrea

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