Variant report

Variant	rs13240138
Chromosome Location	chr7:6050825-6050826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:6050512-6051405	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:6050558-6051831	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr7:6050449-6051640	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr7:6050768-6050963	HepG2	liver:	n/a	n/a
5	POLR2A	chr7:6050816-6050949	HepG2	liver:	n/a	n/a
6	CTCF	chr7:6050800-6050950	A549	lung:	n/a	n/a
7	POLR2A	chr7:6049752-6051772	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr7:6050407-6051477	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr7:6050597-6051126	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6049210..6050889-chr7:6069296..6071152,2	MCF-7	breast:
2	chr7:6049838..6052195-chr7:6053288..6054937,2	K562	blood:
3	chr7:6049211..6051236-chr7:6138312..6140816,2	MCF-7	breast:
4	chr7:6048500..6051239-chr7:6096959..6099959,3	K562	blood:
5	chr7:6047930..6051239-chr7:6095534..6098918,6	K562	blood:
6	chr7:6047026..6051403-chr7:6141746..6146462,7	K562	blood:
7	chr7:6049082..6051960-chr7:6388689..6390680,2	MCF-7	breast:
8	chr7:6050222..6054296-chr7:6073659..6078644,4	K562	blood:
9	chr7:6049571..6051415-chr7:6054993..6057301,2	K562	blood:
10	chr7:6048974..6052104-chr7:6066823..6070557,3	K562	blood:
11	chr7:6049454..6051152-chr7:6143621..6146220,2	MCF-7	breast:
12	chr7:6049165..6051056-chr7:6063162..6065700,2	K562	blood:

No data

Variant related genes	Relation type
PMS2	TF binding region
ENSG00000157999	Chromatin interaction
ENSG00000252929	Chromatin interaction
ENSG00000106346	Chromatin interaction
ENSG00000207217	Chromatin interaction
ENSG00000086232	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12702460	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702461	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702462	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702463	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702464	0.90[ASN][1000 genomes]
rs12702468	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13245536	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13311041	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1860462	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1986625	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2009115	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286680	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34197105	0.90[ASN][1000 genomes]
rs3735296	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3779107	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59901370	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6463525	0.93[ASN][1000 genomes]
rs6949598	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6953340	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6964944	0.83[EUR][1000 genomes]
rs6973250	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6974270	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71524066	0.81[EUR][1000 genomes]
rs7781199	0.85[EUR][1000 genomes]
rs7788051	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7799214	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7805798	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
2	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
3	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
5	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
6	nsv1034215	chr7:5748982-6056619	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
7	nsv1016690	chr7:5749222-6056619	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
8	nsv1027679	chr7:5760731-6056619	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
10	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
11	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
12	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
13	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
14	nsv830894	chr7:5889658-6072215	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
15	nsv1034916	chr7:5934780-6158970	Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
16	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
17	nsv605998	chr7:6035065-6102034	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1018388	chr7:6038713-6131169	Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers 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 miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6049200-6051200	Weak transcription	Stomach Mucosa	stomach
2	chr7:6049200-6061800	Weak transcription	Fetal Brain Male	brain
3	chr7:6049400-6051000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:6049400-6051200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr7:6049400-6052200	Weak transcription	Esophagus	oesophagus
6	chr7:6049400-6054600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:6049400-6054600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:6049400-6054800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr7:6049400-6054800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:6049400-6054800	Weak transcription	Gastric	stomach
11	chr7:6049400-6054800	Weak transcription	Spleen	Spleen
12	chr7:6049400-6055400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:6049400-6055400	Weak transcription	Aorta	Aorta
14	chr7:6049400-6055800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr7:6049400-6055800	Weak transcription	Fetal Lung	lung
16	chr7:6049400-6056000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:6049400-6056000	Weak transcription	Thymus	Thymus
18	chr7:6049400-6061400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr7:6049400-6098000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr7:6049600-6051200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr7:6049600-6052200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:6049600-6052200	Weak transcription	Colonic Mucosa	Colon
23	chr7:6049600-6052200	Weak transcription	Fetal Stomach	stomach
24	chr7:6049600-6052200	Weak transcription	Pancreas	Pancrea
25	chr7:6049600-6054800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr7:6049600-6060400	Weak transcription	Fetal Kidney	kidney
27	chr7:6049600-6060600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr7:6049800-6052200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:6049800-6053400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr7:6049800-6054600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:6049800-6054600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr7:6049800-6054800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:6049800-6055400	Weak transcription	Right Ventricle	heart
34	chr7:6050000-6051000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr7:6050000-6051000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:6050000-6051200	Enhancers	Brain Cingulate Gyrus	brain
37	chr7:6050000-6051200	Enhancers	Fetal Heart	heart
38	chr7:6050000-6051400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr7:6050000-6051800	Weak transcription	Fetal Brain Female	brain
40	chr7:6050000-6052000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:6050000-6052000	Weak transcription	Placenta	Placenta
42	chr7:6050000-6052200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr7:6050000-6052400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:6050000-6052600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr7:6050000-6052800	Enhancers	Adipose Nuclei	Adipose
46	chr7:6050000-6054400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr7:6050000-6054600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr7:6050000-6054600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr7:6050000-6054600	Weak transcription	Primary T cells from cord blood	blood
50	chr7:6050000-6054600	Weak transcription	Primary T cells fromperipheralblood	blood

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