Variant report

Variant	rs9462164
Chromosome Location	chr6:36203710-36203711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36096010..36098478-chr6:36202902..36204616,2	MCF-7	breast:
2	chr6:36203266..36205122-chr6:36239627..36241788,2	K562	blood:
3	chr6:36200507..36203942-chr6:36214708..36217317,3	K562	blood:
4	chr6:36201960..36204325-chr6:36233280..36235453,2	K562	blood:
5	chr6:36202408..36205069-chr6:36211679..36213186,2	K562	blood:
6	chr6:36168943..36170715-chr6:36202531..36204301,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156711	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2239798	0.94[ASW][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4236049	0.83[ASW][hapmap];0.83[CHB][hapmap]
rs4395718	0.88[CHB][hapmap]
rs59200830	0.97[AFR][1000 genomes]
rs9462162	0.84[AFR][1000 genomes]
rs9462165	0.94[ASW][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9470229	0.94[ASW][hapmap];0.89[CHD][hapmap];1.00[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs9470230	0.94[ASW][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs9470233	1.00[ASW][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs9470234	0.83[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9470235	0.82[CHB][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9462164	MDGA1	cis	parietal	SCAN
rs9462164	MAPK14	cis	cerebellum	SCAN
rs9462164	KCNK17	cis	cerebellum	SCAN
rs9462164	MAPK13	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36174000-36204600	Strong transcription	Primary T cells from cord blood	blood
2	chr6:36185800-36210600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:36189000-36204800	Strong transcription	Fetal Stomach	stomach
4	chr6:36189600-36204400	Strong transcription	Brain Germinal Matrix	brain
5	chr6:36189800-36203800	Strong transcription	Stomach Smooth Muscle	stomach
6	chr6:36193800-36206800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:36194600-36207200	Weak transcription	Fetal Heart	heart
8	chr6:36195200-36204600	Strong transcription	Fetal Brain Female	brain
9	chr6:36196000-36209200	Weak transcription	K562	blood
10	chr6:36198000-36204400	Weak transcription	NH-A	brain
11	chr6:36198400-36209200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:36198400-36211400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:36198600-36204400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:36198800-36209600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:36199000-36210800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:36199200-36204400	Strong transcription	Fetal Intestine Small	intestine
17	chr6:36199400-36207400	Weak transcription	Brain Substantia Nigra	brain
18	chr6:36199400-36211000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:36199600-36205000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:36199600-36205800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:36199600-36209200	Weak transcription	GM12878-XiMat	blood
22	chr6:36199800-36211400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:36199800-36216200	Weak transcription	NHLF	lung
24	chr6:36200000-36203800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:36200000-36204000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:36200200-36204000	Weak transcription	Small Intestine	intestine
27	chr6:36200200-36208000	Weak transcription	Esophagus	oesophagus
28	chr6:36200200-36209600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:36200200-36210600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:36200200-36211400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:36200200-36213000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:36200400-36207400	Weak transcription	HepG2	liver
33	chr6:36200600-36204400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:36201200-36209200	Weak transcription	Right Ventricle	heart
35	chr6:36201200-36211400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:36201200-36212200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:36201200-36212800	Weak transcription	Fetal Lung	lung
38	chr6:36201200-36215400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:36201400-36204200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:36201400-36205000	Weak transcription	Osteobl	bone
41	chr6:36201400-36207000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:36201400-36209000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:36201400-36209200	Weak transcription	Left Ventricle	heart
44	chr6:36201400-36211400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:36201400-36215600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:36201400-36216600	Weak transcription	Aorta	Aorta
47	chr6:36201600-36204600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr6:36201600-36209000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:36201600-36209600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:36201600-36209600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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