Variant report

Variant	rs748408
Chromosome Location	chr6:36942746-36942747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:36942663-36943242	K562	blood:	n/a	n/a
2	POLR2A	chr6:36941286-36946658	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:36941966-36942917	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:36942657-36942759	A549	lung:	n/a	n/a
5	POLR2A	chr6:36942524-36942997	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36938832..36941814-chr6:36942476..36945654,4	MCF-7	breast:
2	chr6:36941974..36945038-chr6:36952808..36956933,4	MCF-7	breast:

Variant related genes	Relation type
MTCH1	TF binding region
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2293383	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2293385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909991	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918432	1.00[ASW][hapmap]
rs6927651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748409	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs753634	0.81[ASW][hapmap]
rs831506	0.81[CHD][hapmap];0.93[GIH][hapmap];0.81[ASN][1000 genomes]
rs9296205	0.86[LWK][hapmap];0.84[YRI][hapmap]
rs9462250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv5263	chr6:36941625-36972109	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
5	esv988069	chr6:36942299-36951067	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs748408	PI16	cis	parietal	SCAN
rs748408	TSPO2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36931800-36948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:36932400-36946800	Strong transcription	Fetal Brain Female	brain
3	chr6:36932400-36951800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:36932800-36947400	Strong transcription	Fetal Stomach	stomach
5	chr6:36933800-36946800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:36933800-36946800	Strong transcription	Brain Anterior Caudate	brain
7	chr6:36933800-36947200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:36934000-36946600	Strong transcription	Thymus	Thymus
9	chr6:36934000-36946800	Strong transcription	Primary T cells from cord blood	blood
10	chr6:36934000-36946800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr6:36934000-36946800	Strong transcription	Colon Smooth Muscle	Colon
12	chr6:36934000-36949600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:36934000-36951600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:36934200-36946600	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:36934200-36946600	Strong transcription	NHDF-Ad	bronchial
16	chr6:36934200-36946800	Strong transcription	Brain Germinal Matrix	brain
17	chr6:36934200-36947000	Strong transcription	Osteobl	bone
18	chr6:36934200-36947200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:36934200-36947400	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:36934200-36949200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:36934200-36950400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:36934400-36943000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:36934400-36946000	Strong transcription	Primary B cells from cord blood	blood
24	chr6:36934400-36946400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:36934400-36946600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:36934400-36946600	Strong transcription	Aorta	Aorta
27	chr6:36934400-36946600	Strong transcription	Brain Cingulate Gyrus	brain
28	chr6:36934400-36946600	Strong transcription	Colonic Mucosa	Colon
29	chr6:36934400-36947200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:36934400-36947200	Strong transcription	NHLF	lung
31	chr6:36934400-36947400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr6:36934400-36947800	Strong transcription	Dnd41	blood
33	chr6:36934400-36949200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:36934600-36947200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:36934600-36947400	Strong transcription	NH-A	brain
36	chr6:36934600-36947600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr6:36934600-36949200	Strong transcription	Placenta	Placenta
38	chr6:36934800-36945400	Strong transcription	Brain Angular Gyrus	brain
39	chr6:36934800-36946800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:36934800-36947000	Strong transcription	Liver	Liver
41	chr6:36934800-36949600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr6:36935000-36943000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:36935000-36946200	Strong transcription	Fetal Lung	lung
44	chr6:36935000-36946400	Strong transcription	HSMMtube	muscle
45	chr6:36935000-36946600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:36935000-36946600	Strong transcription	Pancreas	Pancrea
47	chr6:36935000-36946600	Strong transcription	Rectal Smooth Muscle	rectum
48	chr6:36935000-36946600	Strong transcription	HUVEC	blood vessel
49	chr6:36935000-36946800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr6:36935000-36947000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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