Variant report

Variant	rs56354402
Chromosome Location	chr7:6050196-6050197
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr7:6049983-6050449	HL-60	blood:	n/a	n/a
2	POLR2A	chr7:6049752-6051772	PANC-1	pancreas:	n/a	n/a
3	RCOR1	chr7:6050049-6050244	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6047579..6050679-chr7:6097211..6100186,3	MCF-7	breast:
2	chr7:6049210..6050889-chr7:6069296..6071152,2	MCF-7	breast:
3	chr7:6046967..6050535-chr7:6141219..6149580,10	K562	blood:
4	chr7:6049838..6052195-chr7:6053288..6054937,2	K562	blood:
5	chr7:6049211..6051236-chr7:6138312..6140816,2	MCF-7	breast:
6	chr7:6048500..6051239-chr7:6096959..6099959,3	K562	blood:
7	chr7:6047930..6051239-chr7:6095534..6098918,6	K562	blood:
8	chr7:6047026..6051403-chr7:6141746..6146462,7	K562	blood:
9	chr7:6049082..6051960-chr7:6388689..6390680,2	MCF-7	breast:
10	chr7:6047922..6050389-chr7:6388573..6391369,3	K562	blood:
11	chr7:6049571..6051415-chr7:6054993..6057301,2	K562	blood:
12	chr7:6048974..6052104-chr7:6066823..6070557,3	K562	blood:
13	chr7:6049454..6051152-chr7:6143621..6146220,2	MCF-7	breast:
14	chr7:6049165..6051056-chr7:6063162..6065700,2	K562	blood:

No data

Variant related genes	Relation type
PMS2	TF binding region
ENSG00000178397	Chromatin interaction
ENSG00000157999	Chromatin interaction
ENSG00000252929	Chromatin interaction
ENSG00000086232	Chromatin interaction
ENSG00000207217	Chromatin interaction
ENSG00000106346	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10249956	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12333405	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12334093	0.81[EUR][1000 genomes]
rs1860459	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41280717	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56000981	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56223935	0.81[EUR][1000 genomes]
rs59790240	0.83[EUR][1000 genomes]
rs73056639	0.82[EUR][1000 genomes]
rs73056648	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73056662	0.85[AMR][1000 genomes];0.81[EUR][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	chr7:6047000-6050200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:6047000-6050200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr7:6047200-6050200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:6047600-6050200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr7:6047600-6050200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:6047600-6050400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:6047800-6050200	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr7:6047800-6050200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr7:6047800-6050200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:6047800-6050200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:6047800-6050400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr7:6047800-6050400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:6047800-6050400	Active TSS	GM12878-XiMat	blood
14	chr7:6048000-6050800	Active TSS	Psoas Muscle	Psoas
15	chr7:6048200-6050200	Active TSS	Duodenum Mucosa	Duodenum
16	chr7:6048200-6050200	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr7:6048200-6050200	Active TSS	HUVEC	blood vessel
18	chr7:6048600-6050200	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr7:6049200-6050200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:6049200-6051200	Weak transcription	Stomach Mucosa	stomach
21	chr7:6049200-6061800	Weak transcription	Fetal Brain Male	brain
22	chr7:6049400-6050200	Enhancers	Primary B cells from cord blood	blood
23	chr7:6049400-6050400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:6049400-6050400	Weak transcription	Lung	lung
25	chr7:6049400-6050400	Weak transcription	Small Intestine	intestine
26	chr7:6049400-6050600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:6049400-6050600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr7:6049400-6050800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:6049400-6050800	Enhancers	Liver	Liver
30	chr7:6049400-6051000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:6049400-6051200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:6049400-6052200	Weak transcription	Esophagus	oesophagus
33	chr7:6049400-6054600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr7:6049400-6054600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr7:6049400-6054800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr7:6049400-6054800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr7:6049400-6054800	Weak transcription	Gastric	stomach
38	chr7:6049400-6054800	Weak transcription	Spleen	Spleen
39	chr7:6049400-6055400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr7:6049400-6055400	Weak transcription	Aorta	Aorta
41	chr7:6049400-6055800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:6049400-6055800	Weak transcription	Fetal Lung	lung
43	chr7:6049400-6056000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:6049400-6056000	Weak transcription	Thymus	Thymus
45	chr7:6049400-6061400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr7:6049400-6098000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr7:6049600-6050200	Weak transcription	Left Ventricle	heart
48	chr7:6049600-6050200	Flanking Active TSS	Dnd41	blood
49	chr7:6049600-6050400	Enhancers	Brain Angular Gyrus	brain
50	chr7:6049600-6050600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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