Variant report

Variant	rs753634
Chromosome Location	chr6:36934694-36934695
allele	A/T
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: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1023037	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12191672	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199301	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs17624546	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs17624895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2177845	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2293388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2293389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3778022	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3778024	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs3778026	0.86[EUR][1000 genomes]
rs3798477	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3798478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4585544	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901560	0.80[GIH][hapmap];0.83[MEX][hapmap]
rs726819	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs734905	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748408	0.81[ASW][hapmap]
rs753635	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	0.93[GIH][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9357232	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380628	0.83[AMR][1000 genomes];0.80[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs753634	PI16	cis	cerebellum	SCAN
rs753634	LPAR6	trans	lymphoblastoid	seeQTL
rs753634	PI16	cis	parietal	SCAN
rs753634	MAPK13	cis	lymphoblastoid	seeQTL
rs753634	C10orf116	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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