Variant report

Variant	rs7784748
Chromosome Location	chr7:4784652-4784653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:4769819..4771517-chr7:4783314..4786032,2	MCF-7	breast:
2	chr7:4776716..4781716-chr7:4782818..4787338,6	MCF-7	breast:
3	chr7:4721996..4723803-chr7:4781821..4784827,3	MCF-7	breast:
4	chr7:4782605..4786224-chr7:4813010..4816039,5	K562	blood:
5	chr7:4784548..4788460-chr7:4798127..4799937,3	MCF-7	breast:
6	chr7:4782540..4785616-chr7:4814219..4816404,3	MCF-7	breast:
7	chr7:4777751..4781095-chr7:4782680..4786251,6	K562	blood:
8	chr7:4783269..4785885-chr7:4788147..4790015,2	K562	blood:
9	chr7:4720242..4723190-chr7:4783988..4786279,2	K562	blood:
10	chr18:3451055..3451597-chr7:4784533..4785073,2	Hela-S3	cervix:
11	chr7:4723633..4728859-chr7:4783438..4786381,5	K562	blood:
12	chr7:4784407..4787081-chr7:4798236..4801069,2	K562	blood:
13	chr7:4783569..4786277-chr7:4791910..4794982,3	K562	blood:
14	chr7:4680522..4682464-chr7:4783695..4785954,3	MCF-7	breast:
15	chr7:4762980..4766999-chr7:4782747..4785912,5	MCF-7	breast:
16	chr7:4771743..4774713-chr7:4783422..4786273,3	MCF-7	breast:
17	chr7:4670793..4673336-chr7:4784498..4786362,2	K562	blood:
18	chr7:4762343..4766286-chr7:4781806..4786084,5	MCF-7	breast:
19	chr7:4718155..4726493-chr7:4775257..4787798,22	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000242802	Chromatin interaction
ENSG00000177426	Chromatin interaction
ENSG00000164916	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10228886	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs10232008	0.96[ASN][1000 genomes]
rs10257680	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10261971	0.88[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs10262715	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10277273	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12701913	0.98[ASN][1000 genomes]
rs13232425	0.86[ASN][1000 genomes]
rs3087749	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs35735269	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4720401	0.82[JPT][hapmap]
rs4724033	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6463014	0.83[ASN][1000 genomes]
rs6463019	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6975499	0.83[ASN][1000 genomes]
rs7781115	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7781456	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs7786525	0.82[ASN][1000 genomes]
rs7793919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.84[EUR][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	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv887377	chr7:4730535-4862259	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv887378	chr7:4730535-4929721	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv887379	chr7:4749527-4828593	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv887380	chr7:4760124-4929721	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv471293	chr7:4764861-4885221	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv887381	chr7:4769030-4880954	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer 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 miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7784748	PMS2CL	cis	cerebellum	SCAN
rs7784748	ZNF12	cis	parietal	SCAN
rs7784748	RAC1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4779600-4785400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:4782000-4785200	Weak transcription	Aorta	Aorta
3	chr7:4782600-4785600	Enhancers	Fetal Kidney	kidney
4	chr7:4782600-4785600	Enhancers	NH-A	brain
5	chr7:4782600-4786400	Weak transcription	Ovary	ovary
6	chr7:4782800-4784800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:4783000-4785200	Enhancers	Fetal Lung	lung
8	chr7:4783000-4785400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:4783000-4785400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:4783200-4785000	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr7:4783200-4785200	Enhancers	Fetal Brain Male	brain
12	chr7:4783200-4788200	Enhancers	Fetal Heart	heart
13	chr7:4783400-4791000	Weak transcription	Gastric	stomach
14	chr7:4783600-4785200	Enhancers	HMEC	breast
15	chr7:4784000-4784800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr7:4784000-4784800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:4784000-4784800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr7:4784000-4784800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:4784000-4784800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr7:4784000-4784800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr7:4784000-4784800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr7:4784000-4784800	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr7:4784000-4784800	Enhancers	Spleen	Spleen
24	chr7:4784000-4784800	Flanking Active TSS	GM12878-XiMat	blood
25	chr7:4784000-4785000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
26	chr7:4784000-4785000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:4784000-4785000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr7:4784000-4785000	Enhancers	Pancreas	Pancrea
29	chr7:4784000-4785200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
30	chr7:4784000-4785200	Flanking Active TSS	Thymus	Thymus
31	chr7:4784000-4785600	Flanking Active TSS	Dnd41	blood
32	chr7:4784000-4785600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr7:4784000-4786000	Flanking Active TSS	Fetal Thymus	thymus
34	chr7:4784000-4786200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr7:4784000-4786400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:4784000-4786600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr7:4784000-4786600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr7:4784000-4787000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:4784200-4784800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:4784200-4784800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr7:4784200-4784800	Flanking Active TSS	Fetal Stomach	stomach
42	chr7:4784200-4784800	Flanking Active TSS	HUVEC	blood vessel
43	chr7:4784200-4785000	Flanking Active TSS	Fetal Brain Female	brain
44	chr7:4784200-4785000	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr7:4784200-4785000	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr7:4784200-4785200	Active TSS	H9 Cell Line	embryonic stem cell
47	chr7:4784200-4785200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr7:4784200-4785600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr7:4784200-4785600	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr7:4784200-4786200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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