Variant report

Variant	rs753635
Chromosome Location	chr6:36934762-36934763
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36930754..36936310-chr6:36950773..36956274,7	MCF-7	breast:
2	chr6:36933241..36935002-chr6:36938613..36940205,2	MCF-7	breast:
3	chr6:36856253..36859191-chr6:36932885..36935045,2	K562	blood:
4	chr6:36934586..36938326-chr6:36939684..36941889,3	MCF-7	breast:
5	chr6:36921333..36923898-chr6:36932868..36934927,2	K562	blood:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction
ENSG00000164530	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1023037	0.89[ASN][1000 genomes]
rs12191672	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199301	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs17624546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17624895	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2177845	0.89[ASN][1000 genomes]
rs2293388	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2293389	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs3778022	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs3778024	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3778026	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3798477	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3798478	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs4585544	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901560	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs726819	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs734905	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753634	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755143	0.83[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9357232	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380628	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv525288	chr6:36934244-36937647	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs753635	MAPK13	cis	lymphoblastoid	seeQTL
rs753635	C10orf116	trans	lymphoblastoid	seeQTL
rs753635	PI16	cis	cerebellum	SCAN
rs753635	LPAR6	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36928200-36935200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:36928600-36935000	Weak transcription	HSMMtube	muscle
3	chr6:36928600-36935400	Weak transcription	Small Intestine	intestine
4	chr6:36928800-36935000	Weak transcription	HUVEC	blood vessel
5	chr6:36929000-36934800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:36929000-36935200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:36929000-36935400	Weak transcription	Ovary	ovary
8	chr6:36929000-36935400	Weak transcription	A549	lung
9	chr6:36929400-36935200	Weak transcription	K562	blood
10	chr6:36929600-36936800	Weak transcription	Hela-S3	cervix
11	chr6:36931400-36935000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:36931400-36935000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:36931400-36935000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:36931400-36935600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:36931600-36934800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:36931600-36935000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:36931600-36935200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:36931600-36935200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:36931600-36935200	Weak transcription	HMEC	breast
20	chr6:36931600-36935400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:36931600-36935400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:36931600-36936200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:36931600-36938600	Weak transcription	Fetal Brain Male	brain
24	chr6:36931800-36934800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:36931800-36935000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:36931800-36935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:36931800-36948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:36932000-36935000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr6:36932000-36935200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:36932200-36934800	Weak transcription	Brain Angular Gyrus	brain
31	chr6:36932200-36934800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:36932200-36935000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:36932200-36935000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:36932200-36935400	Weak transcription	GM12878-XiMat	blood
35	chr6:36932400-36946800	Strong transcription	Fetal Brain Female	brain
36	chr6:36932400-36951800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:36932600-36935000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:36932600-36935000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:36932600-36935000	Weak transcription	Brain Substantia Nigra	brain
40	chr6:36932600-36935000	Weak transcription	Esophagus	oesophagus
41	chr6:36932600-36935000	Weak transcription	HepG2	liver
42	chr6:36932600-36936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:36932800-36947400	Strong transcription	Fetal Stomach	stomach
44	chr6:36933000-36935400	Weak transcription	Fetal Kidney	kidney
45	chr6:36933000-36935600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:36933000-36936400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr6:36933200-36934800	Weak transcription	Liver	Liver
48	chr6:36933200-36935000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:36933200-36935000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr6:36933200-36935000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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