Variant report

Variant	rs59901370
Chromosome Location	chr7:6055084-6055085
allele	G/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	chr7:6054577-6055086	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:6054542-6055156	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr7:6054997-6055435	HepG2	liver:	n/a	n/a
4	PAX5	chr7:6055035-6055779	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6054308..6057610-chr7:6144384..6145966,3	K562	blood:
2	chr7:6054346..6056159-chr7:6142852..6144380,2	K562	blood:
3	chr7:6046629..6049121-chr7:6054916..6059212,5	K562	blood:
4	chr7:6051523..6054079-chr7:6054548..6056374,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207217	TF binding region
ENSG00000106305	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000106346	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12702460	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12702461	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12702462	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12702463	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12702464	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12702468	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13240138	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13245536	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13311041	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1860462	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1986625	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009115	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286680	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34197105	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3735296	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3779107	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3779109	0.84[AFR][1000 genomes]
rs6463525	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6949598	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6953340	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6973250	0.89[EUR][1000 genomes]
rs6974270	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7781199	0.89[EUR][1000 genomes]
rs7788051	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799214	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7805798	0.87[EUR][1000 genomes];0.86[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	chr7:6049200-6061800	Weak transcription	Fetal Brain Male	brain
2	chr7:6049400-6055400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:6049400-6055400	Weak transcription	Aorta	Aorta
4	chr7:6049400-6055800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:6049400-6055800	Weak transcription	Fetal Lung	lung
6	chr7:6049400-6056000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:6049400-6056000	Weak transcription	Thymus	Thymus
8	chr7:6049400-6061400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr7:6049400-6098000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr7:6049600-6060400	Weak transcription	Fetal Kidney	kidney
11	chr7:6049600-6060600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr7:6049800-6055400	Weak transcription	Right Ventricle	heart
13	chr7:6050000-6055400	Weak transcription	Right Atrium	heart
14	chr7:6050000-6057200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:6050000-6097800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:6050400-6065600	Strong transcription	Lung	lung
17	chr7:6050400-6065800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:6050400-6089400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:6050400-6095400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:6050400-6095600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:6050600-6055200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr7:6050600-6057600	Strong transcription	Primary hematopoietic stem cells	blood
23	chr7:6050600-6070000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr7:6050600-6091000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:6050800-6062000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr7:6050800-6091000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:6050800-6095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:6051000-6055400	Weak transcription	Brain Angular Gyrus	brain
29	chr7:6051000-6062200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:6051000-6095200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr7:6051200-6055400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:6051200-6055400	Weak transcription	Fetal Heart	heart
33	chr7:6051200-6055400	Weak transcription	NHLF	lung
34	chr7:6051400-6055200	Weak transcription	NHDF-Ad	bronchial
35	chr7:6051400-6055400	Weak transcription	NH-A	brain
36	chr7:6051800-6055800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:6051800-6089600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:6052200-6089400	Strong transcription	Fetal Stomach	stomach
39	chr7:6052400-6062000	Weak transcription	Small Intestine	intestine
40	chr7:6052600-6055200	Enhancers	Psoas Muscle	Psoas
41	chr7:6052600-6094600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:6052800-6055400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
43	chr7:6052800-6055800	Weak transcription	Brain Hippocampus Middle	brain
44	chr7:6053000-6055400	Weak transcription	Primary B cells from cord blood	blood
45	chr7:6053000-6055400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr7:6053000-6095000	Strong transcription	Fetal Intestine Small	intestine
47	chr7:6053400-6055400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:6053400-6055600	Weak transcription	Pancreas	Pancrea
49	chr7:6053400-6055800	Weak transcription	Colonic Mucosa	Colon
50	chr7:6054000-6066000	Strong transcription	Stomach Smooth Muscle	stomach

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