Variant report

Variant	rs6926250
Chromosome Location	chr6:131302473-131302474
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	POLR2A	chr6:131302451-131302918	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131301483..131303877-chr6:131310985..131313836,2	MCF-7	breast:

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12525986	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13437326	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs17178878	0.83[AMR][1000 genomes]
rs17179123	0.80[AMR][1000 genomes]
rs17180687	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs17770255	0.87[CEU][hapmap]
rs17784418	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs17785507	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs1811949	1.00[CHB][hapmap]
rs2095961	0.82[CHB][hapmap]
rs2297853	1.00[CHB][hapmap]
rs28482889	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs34899420	0.80[AMR][1000 genomes]
rs3777434	0.83[CEU][hapmap]
rs3777435	0.83[CEU][hapmap]
rs3777436	0.83[CEU][hapmap]
rs4895901	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs4895903	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4895907	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs4895908	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs4897473	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs4897478	0.83[AMR][1000 genomes]
rs4897484	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs4897485	0.81[CEU][hapmap]
rs56173113	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62423581	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6906059	0.80[AMR][1000 genomes]
rs6906478	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs6921396	1.00[CHB][hapmap]
rs6922045	1.00[CHB][hapmap]
rs6922177	0.82[CHB][hapmap]
rs6928920	1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs6931804	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6935108	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs7741148	1.00[CHB][hapmap]
rs7755720	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7761311	0.82[CHB][hapmap]
rs7769678	1.00[CHB][hapmap]
rs7775013	0.83[CEU][hapmap]
rs872576	1.00[CHB][hapmap]
rs9321263	0.82[CHB][hapmap]
rs9372985	0.82[CHB][hapmap]
rs9385568	1.00[CHB][hapmap]
rs9388861	0.81[CEU][hapmap]
rs942	1.00[CHB][hapmap]
rs9483206	1.00[CHB][hapmap]
rs954211	0.86[CEU][hapmap];0.82[CHB][hapmap]

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
rs6926250	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131288200-131306600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:131291800-131306200	Weak transcription	Fetal Intestine Small	intestine
3	chr6:131292400-131306400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:131296800-131302600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:131297600-131302800	Enhancers	Brain Cingulate Gyrus	brain
6	chr6:131298800-131314800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:131299000-131306200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:131299000-131309800	Weak transcription	HepG2	liver
9	chr6:131299200-131304600	Enhancers	Fetal Lung	lung
10	chr6:131299400-131303600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:131300200-131302600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:131300200-131304000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:131300400-131302600	Weak transcription	Brain Angular Gyrus	brain
14	chr6:131300400-131302600	Weak transcription	Brain Anterior Caudate	brain
15	chr6:131300400-131312200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:131300400-131314600	Weak transcription	Small Intestine	intestine
17	chr6:131300800-131303800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:131301000-131305000	Enhancers	Dnd41	blood
19	chr6:131301200-131304600	Enhancers	Fetal Kidney	kidney
20	chr6:131301400-131302800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr6:131301400-131303000	Enhancers	Primary T cells from cord blood	blood
22	chr6:131301400-131303400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:131301600-131302600	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:131301600-131302600	Weak transcription	Brain Substantia Nigra	brain
25	chr6:131301800-131302600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:131301800-131302600	Enhancers	Psoas Muscle	Psoas
27	chr6:131301800-131305000	Enhancers	Colon Smooth Muscle	Colon
28	chr6:131301800-131306200	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:131302000-131302800	Enhancers	NHLF	lung
30	chr6:131302000-131303400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:131302000-131304000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:131302200-131302600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:131302200-131302600	Weak transcription	Thymus	Thymus
34	chr6:131302200-131302800	Enhancers	HSMM	muscle
35	chr6:131302200-131303400	Enhancers	Brain Germinal Matrix	brain
36	chr6:131302200-131304000	Weak transcription	K562	blood
37	chr6:131302200-131304400	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr6:131302400-131302600	Enhancers	Fetal Stomach	stomach
39	chr6:131302400-131302800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:131302400-131303600	Enhancers	NHDF-Ad	bronchial
41	chr6:131302400-131304200	Enhancers	Adipose Nuclei	Adipose
42	chr6:131302400-131304800	Enhancers	Rectal Smooth Muscle	rectum
43	chr6:131302400-131306400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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