Variant report

Variant	rs507672
Chromosome Location	chr11:65767153-65767154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65767124-65767198	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65629227..65631870-chr11:65766567..65769342,2	MCF-7	breast:
2	chr11:65636578..65639381-chr11:65766938..65769474,2	MCF-7	breast:
3	chr11:65766270..65769793-chr11:65817988..65822487,7	MCF-7	breast:
4	chr11:65764048..65767930-chr11:65768133..65771443,5	MCF-7	breast:
5	chr11:65546195..65548031-chr11:65766372..65768235,2	K562	blood:

No data

Variant related genes	Relation type
BANF1	TF binding region
ENSG00000172732	Chromatin interaction
ENSG00000172638	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000175827	Chromatin interaction
ENSG00000238752	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11227377	0.86[AMR][1000 genomes]
rs1151510	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151511	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1151514	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1191716	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1192184	0.99[EUR][1000 genomes]
rs1204011	1.00[EUR][1000 genomes]
rs1786171	0.84[AMR][1000 genomes]
rs1786172	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1786174	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs502363	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506873	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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]
rs522553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534201	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540584	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs543952	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs548435	0.83[EUR][1000 genomes]
rs548495	0.98[EUR][1000 genomes]
rs549334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559161	0.86[AMR][1000 genomes]
rs586921	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs590531	1.00[EUR][1000 genomes]
rs610497	0.89[GIH][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs615646	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs616073	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs619701	1.00[EUR][1000 genomes]
rs622779	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs632640	0.83[EUR][1000 genomes]
rs645571	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs668210	0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs677350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684546	0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7933510	0.83[EUR][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	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
6	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs507672	SCGB1D1	cis	cerebellum	SCAN
rs507672	SNX32	cis	parietal	SCAN
rs507672	MRPL11	cis	cerebellum	SCAN
rs507672	RAD9A	cis	cerebellum	SCAN
rs507672	RTN3	cis	parietal	SCAN
rs507672	SNORD26	cis	parietal	SCAN
rs507672	PACS1	cis	cerebellum	SCAN
rs507672	PCNXL3	cis	cerebellum	SCAN
rs507672	DKFZp761E198	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65730600-65767800	Weak transcription	Right Atrium	heart
2	chr11:65736400-65767400	Weak transcription	Psoas Muscle	Psoas
3	chr11:65757400-65767600	Weak transcription	Stomach Mucosa	stomach
4	chr11:65761200-65767400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:65761200-65767800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:65761800-65767400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr11:65761800-65767600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:65761800-65767600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr11:65762000-65767400	Strong transcription	Fetal Thymus	thymus
10	chr11:65762200-65767600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:65762200-65767600	Strong transcription	Fetal Stomach	stomach
12	chr11:65762400-65767600	Strong transcription	Primary T cells from cord blood	blood
13	chr11:65762400-65767600	Strong transcription	Thymus	Thymus
14	chr11:65762400-65767800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:65762400-65767800	Strong transcription	NHEK	skin
16	chr11:65762600-65767400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:65762800-65767600	Strong transcription	Fetal Intestine Small	intestine
18	chr11:65763000-65767800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:65763600-65767600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:65764000-65767200	Strong transcription	Brain Germinal Matrix	brain
21	chr11:65764000-65767600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:65764000-65767600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:65764000-65767600	Strong transcription	Brain Substantia Nigra	brain
24	chr11:65764000-65767600	Strong transcription	Placenta	Placenta
25	chr11:65764000-65767800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:65764000-65767800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr11:65764000-65768600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:65764200-65767400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:65764200-65767400	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr11:65764200-65767400	Strong transcription	Liver	Liver
31	chr11:65764200-65767400	Strong transcription	Spleen	Spleen
32	chr11:65764200-65767600	Strong transcription	Primary B cells from cord blood	blood
33	chr11:65764200-65767600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:65764200-65767600	Strong transcription	Adipose Nuclei	Adipose
35	chr11:65764200-65767600	Strong transcription	Brain Anterior Caudate	brain
36	chr11:65764200-65767600	Strong transcription	Colon Smooth Muscle	Colon
37	chr11:65764200-65767600	Strong transcription	Gastric	stomach
38	chr11:65764200-65767600	Strong transcription	Right Ventricle	heart
39	chr11:65764200-65767600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:65764200-65767600	Strong transcription	A549	lung
41	chr11:65764200-65767600	Strong transcription	HMEC	breast
42	chr11:65764200-65767600	Strong transcription	HSMMtube	muscle
43	chr11:65764200-65767800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:65764200-65767800	Strong transcription	Brain Cingulate Gyrus	brain
45	chr11:65764200-65767800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr11:65764200-65767800	Strong transcription	Fetal Muscle Leg	muscle
47	chr11:65764200-65767800	Strong transcription	HUVEC	blood vessel
48	chr11:65764200-65767800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr11:65764200-65767800	Strong transcription	NH-A	brain
50	chr11:65764200-65768000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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