Variant report

Variant	rs6901560
Chromosome Location	chr6:36931994-36931995
allele	C/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	chr6:36930815..36932327-chr6:37373552..37376539,2	K562	blood:
3	chr6:36929829..36933522-chr6:36953197..36956380,5	MCF-7	breast:
4	chr6:36928176..36930778-chr6:36931482..36933887,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164530	Chromatin interaction
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12191672	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs3778022	0.87[GIH][hapmap];0.89[MEX][hapmap]
rs3798478	0.87[GIH][hapmap];0.83[MEX][hapmap]
rs4585544	0.85[AMR][1000 genomes]
rs6914608	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753634	0.80[GIH][hapmap];0.83[MEX][hapmap]
rs753635	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs7755143	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9357232	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs9380627	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6901560	PI16	cis	cerebellum	SCAN
rs6901560	LPAR6	trans	lymphoblastoid	seeQTL
rs6901560	MLN	cis	cerebellum	SCAN
rs6901560	TSPO2	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36927200-36933400	Enhancers	Stomach Mucosa	stomach
2	chr6:36927800-36933200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:36928000-36933600	Enhancers	Primary T cells fromperipheralblood	blood
4	chr6:36928200-36935200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:36928600-36935000	Weak transcription	HSMMtube	muscle
6	chr6:36928600-36935400	Weak transcription	Small Intestine	intestine
7	chr6:36928800-36934000	Weak transcription	HSMM	muscle
8	chr6:36928800-36935000	Weak transcription	HUVEC	blood vessel
9	chr6:36929000-36934200	Weak transcription	Osteobl	bone
10	chr6:36929000-36934400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:36929000-36934800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:36929000-36935200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:36929000-36935400	Weak transcription	Ovary	ovary
14	chr6:36929000-36935400	Weak transcription	A549	lung
15	chr6:36929200-36934600	Weak transcription	NH-A	brain
16	chr6:36929400-36934400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:36929400-36935200	Weak transcription	K562	blood
18	chr6:36929600-36932000	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:36929600-36932200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:36929600-36936800	Weak transcription	Hela-S3	cervix
21	chr6:36929800-36933200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:36930000-36933000	Enhancers	Primary B cells from cord blood	blood
23	chr6:36930400-36933000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:36930400-36933200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:36930600-36932000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:36930600-36932000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:36930600-36932200	Enhancers	GM12878-XiMat	blood
28	chr6:36930600-36932400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:36930600-36932400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:36930600-36933000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr6:36930600-36933000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:36930600-36933000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:36930600-36933000	Enhancers	Dnd41	blood
34	chr6:36930600-36933200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:36930600-36933200	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr6:36930600-36933200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:36930600-36933200	Enhancers	Fetal Heart	heart
38	chr6:36930800-36932400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:36930800-36932600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:36930800-36933200	Enhancers	Primary hematopoietic stem cells	blood
41	chr6:36930800-36933200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:36931000-36932000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:36931000-36932000	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr6:36931000-36932400	Bivalent Enhancer	Fetal Stomach	stomach
45	chr6:36931000-36932400	Enhancers	NHEK	skin
46	chr6:36931000-36932600	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr6:36931000-36932600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:36931000-36932600	Enhancers	Brain Substantia Nigra	brain
49	chr6:36931000-36932600	Enhancers	Esophagus	oesophagus
50	chr6:36931000-36933000	Enhancers	Brain Anterior Caudate	brain

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