Variant report

Variant	rs6457879
Chromosome Location	chr6:36080053-36080054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36077863..36080444-chr6:36082662..36085280,4	K562	blood:
2	chr6:36078019..36080640-chr6:36125434..36127068,2	MCF-7	breast:
3	chr6:36075459..36077532-chr6:36079857..36081490,2	K562	blood:
4	chr6:36072201..36074873-chr6:36079773..36082380,2	MCF-7	breast:
5	chr6:36078755..36080631-chr6:36164137..36165719,2	MCF-7	breast:
6	chr6:36066380..36072646-chr6:36077457..36080962,6	K562	blood:
7	chr6:36078169..36081886-chr6:36162139..36167468,6	K562	blood:
8	chr6:35994681..35997469-chr6:36079865..36081711,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000112062	Chromatin interaction
ENSG00000246982	Chromatin interaction
ENSG00000096070	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10484265	0.86[MEX][hapmap];1.00[MKK][hapmap]
rs1100856	0.81[EUR][1000 genomes]
rs1100857	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1100859	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1100860	0.86[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194501	1.00[CHD][hapmap]
rs17655247	0.86[MEX][hapmap]
rs2815806	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815809	0.88[MEX][hapmap];0.94[TSI][hapmap]
rs707994	1.00[CEU][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73729674	1.00[ASN][1000 genomes]
rs851004	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851008	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851009	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851011	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851012	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851015	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851016	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851021	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851022	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851023	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851025	0.93[EUR][1000 genomes]
rs916344	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916345	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916346	0.81[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6457879	TMEM217	cis	parietal	SCAN
rs6457879	SRPK1	cis	cerebellum	SCAN
rs6457879	MAPK14	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36022000-36088800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:36051600-36088800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:36060600-36080800	Weak transcription	Ovary	ovary
4	chr6:36063200-36080600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:36063400-36080600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr6:36063600-36080800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:36065400-36082600	Weak transcription	Stomach Mucosa	stomach
8	chr6:36067000-36082800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:36067400-36081000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr6:36068000-36091400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:36068200-36081200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:36069000-36081400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:36069200-36081800	Strong transcription	Fetal Intestine Large	intestine
14	chr6:36069400-36080200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:36069400-36080200	Strong transcription	Osteobl	bone
16	chr6:36069400-36083000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:36069600-36081200	Strong transcription	Primary hematopoietic stem cells	blood
18	chr6:36070000-36080600	Strong transcription	Placenta	Placenta
19	chr6:36070000-36082000	Strong transcription	Liver	Liver
20	chr6:36072200-36082800	Weak transcription	Colonic Mucosa	Colon
21	chr6:36073200-36082600	Weak transcription	Fetal Heart	heart
22	chr6:36074600-36080200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:36074600-36080200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:36074600-36081000	Genic enhancers	Fetal Thymus	thymus
25	chr6:36074800-36080600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:36074800-36085400	Strong transcription	Fetal Stomach	stomach
27	chr6:36074800-36085600	Strong transcription	Fetal Intestine Small	intestine
28	chr6:36075000-36080200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:36075000-36080800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:36075200-36080200	Strong transcription	Lung	lung
31	chr6:36075200-36080800	Strong transcription	Stomach Smooth Muscle	stomach
32	chr6:36075200-36081000	Strong transcription	HSMM	muscle
33	chr6:36075400-36082000	Strong transcription	Fetal Lung	lung
34	chr6:36075800-36080600	Genic enhancers	Fetal Muscle Leg	muscle
35	chr6:36076600-36082600	Enhancers	Primary B cells from peripheral blood	blood
36	chr6:36076600-36088200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:36076600-36088600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:36076800-36080200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:36077000-36086200	Weak transcription	Esophagus	oesophagus
40	chr6:36077200-36082600	Weak transcription	Pancreas	Pancrea
41	chr6:36077200-36085800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr6:36077200-36086000	Weak transcription	Small Intestine	intestine
43	chr6:36077200-36088400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:36077200-36088400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:36077200-36088800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:36077200-36088800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:36077200-36088800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:36077200-36094800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:36077200-36096600	Weak transcription	Fetal Brain Female	brain
50	chr6:36077400-36094800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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