Variant report

Variant	rs7337488
Chromosome Location	chr13:50068628-50068629
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr13:50068562-50068868	GM12878	blood:	n/a	n/a
2	SPI1	chr13:50068613-50069143	HL-60	blood:	n/a	chr13:50068930-50068937

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:49993633..49996417-chr13:50068251..50070383,2	K562	blood:
2	chr13:50068064..50069672-chr13:50174689..50176260,2	MCF-7	breast:
3	chr13:50016483..50020444-chr13:50068529..50072853,4	MCF-7	breast:
4	chr13:50016715..50020360-chr13:50068508..50074036,7	MCF-7	breast:
5	chr13:50061049..50067624-chr13:50068104..50073631,8	MCF-7	breast:
6	chr13:50060291..50062533-chr13:50067429..50069545,2	K562	blood:
7	chr13:50020071..50022197-chr13:50067941..50070115,2	K562	blood:
8	chr13:50064832..50068654-chr13:50068754..50072882,4	K562	blood:
9	chr13:50068585..50069355-chr13:50091395..50092213,3	MCF-7	breast:

No data

Variant related genes	Relation type
PHF11	TF binding region
ENSG00000236577	Chromatin interaction
ENSG00000136147	Chromatin interaction
ENSG00000215462	Chromatin interaction
ENSG00000136169	Chromatin interaction
ENSG00000102547	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12050042	0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1543514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1980794	0.84[EUR][1000 genomes]
rs1980795	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs2031532	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2057413	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2407692	0.91[ASN][1000 genomes]
rs2407693	0.95[ASN][1000 genomes]
rs3764085	0.84[EUR][1000 genomes]
rs3764090	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs4142285	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4417458	0.91[ASN][1000 genomes]
rs4942835	0.88[ASN][1000 genomes]
rs6561525	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6561527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561528	0.95[ASN][1000 genomes]
rs6561529	0.95[ASN][1000 genomes]
rs6561531	0.81[ASN][1000 genomes]
rs7321228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7324622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328782	0.95[ASN][1000 genomes]
rs7982297	0.91[ASN][1000 genomes]
rs7992603	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs7996852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs7998660	1.00[JPT][hapmap]
rs8000149	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9316453	0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap]
rs9526564	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535241	0.89[JPT][hapmap]
rs9568223	0.84[EUR][1000 genomes]
rs959421	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv561614	chr13:50042983-50086253	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv561615	chr13:50042983-50086266	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7337488	CAB39L	cis	cerebellum	SCAN
rs7337488	RB1	cis	cerebellum	SCAN
rs7337488	EBPL	cis	parietal	SCAN
rs7337488	SETDB2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50022000-50069000	Weak transcription	Fetal Brain Male	brain
2	chr13:50031800-50068800	Weak transcription	Psoas Muscle	Psoas
3	chr13:50034400-50068800	Weak transcription	NH-A	brain
4	chr13:50037800-50069000	Weak transcription	Colonic Mucosa	Colon
5	chr13:50038000-50068800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:50038400-50069000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr13:50038400-50069400	Weak transcription	Small Intestine	intestine
8	chr13:50038600-50068800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr13:50038800-50069000	Weak transcription	HSMM	muscle
10	chr13:50039200-50068800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr13:50039400-50069200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr13:50041000-50068800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr13:50041400-50069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr13:50049400-50069000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr13:50051400-50069000	Weak transcription	Fetal Brain Female	brain
16	chr13:50051400-50069400	Weak transcription	Gastric	stomach
17	chr13:50051800-50068800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr13:50052000-50068800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr13:50052200-50069200	Weak transcription	Brain Germinal Matrix	brain
20	chr13:50052600-50069000	Weak transcription	Placenta	Placenta
21	chr13:50052600-50069200	Weak transcription	Brain Angular Gyrus	brain
22	chr13:50053000-50069200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:50053000-50069400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr13:50053000-50069400	Weak transcription	Esophagus	oesophagus
25	chr13:50053000-50069400	Weak transcription	Spleen	Spleen
26	chr13:50053400-50069200	Weak transcription	Brain Substantia Nigra	brain
27	chr13:50055400-50069000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr13:50057200-50069200	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:50059000-50069000	Weak transcription	Brain Hippocampus Middle	brain
30	chr13:50059400-50068800	Weak transcription	Brain Anterior Caudate	brain
31	chr13:50060000-50069200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr13:50060800-50069000	Weak transcription	Right Ventricle	heart
33	chr13:50061000-50069000	Weak transcription	Aorta	Aorta
34	chr13:50061000-50069200	Weak transcription	Pancreas	Pancrea
35	chr13:50061000-50069400	Weak transcription	HSMMtube	muscle
36	chr13:50061200-50069200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr13:50061200-50069400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr13:50061200-50069400	Weak transcription	Ovary	ovary
39	chr13:50061200-50069400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr13:50061200-50069800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr13:50061400-50069000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr13:50061600-50069000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr13:50061600-50069400	Weak transcription	Lung	lung
44	chr13:50061800-50069000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr13:50061800-50069000	Weak transcription	Fetal Muscle Leg	muscle
46	chr13:50061800-50069000	Weak transcription	Fetal Stomach	stomach
47	chr13:50062000-50068800	Weak transcription	Fetal Intestine Large	intestine
48	chr13:50062000-50069000	Weak transcription	Left Ventricle	heart
49	chr13:50062200-50069200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr13:50062800-50068800	Weak transcription	Primary B cells from peripheral blood	blood

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