Variant report

Variant	rs3750019
Chromosome Location	chr7:4808678-4808679
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:4796456..4799224-chr7:4806588..4809461,2	MCF-7	breast:
2	chr7:4802110..4804646-chr7:4807009..4808725,2	MCF-7	breast:
3	chr7:4799973..4801525-chr7:4808216..4809966,2	MCF-7	breast:
4	chr7:4808672..4810897-chr7:4813610..4816785,3	MCF-7	breast:
5	chr7:4803027..4805141-chr7:4807600..4810377,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RADIL-1	chr7:4808070-4809064	ENSG00000251104

Variant related genes	Relation type
ENSG00000242802	Chromatin interaction
ENSG00000164916	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10268723	1.00[CHB][hapmap]
rs11628	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11763558	1.00[CHB][hapmap]
rs11768079	1.00[JPT][hapmap]
rs13224156	0.87[ASN][1000 genomes]
rs13236366	0.84[ASN][1000 genomes]
rs17135096	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17135099	0.87[ASN][1000 genomes]
rs17135102	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17135110	1.00[JPT][hapmap]
rs17135128	1.00[JPT][hapmap]
rs17829969	1.00[JPT][hapmap]
rs34217589	0.87[ASN][1000 genomes]
rs35713835	0.84[ASN][1000 genomes]
rs3750012	1.00[JPT][hapmap]
rs3750013	1.00[JPT][hapmap]
rs3750014	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3750015	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3750016	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3750018	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801041	0.84[ASN][1000 genomes]
rs60972000	0.84[ASN][1000 genomes]
rs6463034	1.00[CHB][hapmap]
rs6958952	0.81[ASN][1000 genomes]
rs6963791	1.00[JPT][hapmap]
rs749404	1.00[JPT][hapmap]
rs7777890	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7801122	1.00[JPT][hapmap]
rs7803727	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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
11	nsv823994	chr7:4792385-4928328	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv887382	chr7:4792762-4880954	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv8033	chr7:4802287-5086597	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4785200-4814200	Weak transcription	Fetal Brain Male	brain
2	chr7:4785600-4814400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:4786600-4809000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr7:4787600-4812400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:4788200-4812400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:4788400-4813800	Weak transcription	Right Atrium	heart
7	chr7:4789600-4814400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:4791800-4809000	Strong transcription	NHLF	lung
9	chr7:4793200-4808800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:4793800-4809000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:4794000-4809000	Strong transcription	Liver	Liver
12	chr7:4794200-4809000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:4794200-4814000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:4796600-4814000	Weak transcription	Fetal Kidney	kidney
15	chr7:4798400-4814000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:4798600-4814000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:4799400-4809200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:4800000-4813800	Weak transcription	Primary B cells from cord blood	blood
19	chr7:4800200-4813800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr7:4801000-4814200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr7:4801600-4814400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:4802600-4814200	Weak transcription	Psoas Muscle	Psoas
23	chr7:4802800-4809000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:4803000-4810000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:4803000-4813800	Weak transcription	NHDF-Ad	bronchial
26	chr7:4803000-4814000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr7:4803200-4813200	Weak transcription	K562	blood
28	chr7:4803200-4814200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr7:4803200-4814200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr7:4803400-4809400	Weak transcription	Stomach Mucosa	stomach
31	chr7:4803400-4814000	Weak transcription	Small Intestine	intestine
32	chr7:4803600-4814200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:4803600-4814200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr7:4803600-4814200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:4803800-4809200	Weak transcription	NH-A	brain
36	chr7:4803800-4813600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr7:4803800-4813800	Weak transcription	GM12878-XiMat	blood
38	chr7:4803800-4814200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr7:4803800-4814200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:4804000-4814200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr7:4804200-4814200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:4804400-4813800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr7:4804600-4810600	Weak transcription	Gastric	stomach
44	chr7:4804600-4813800	Weak transcription	Osteobl	bone
45	chr7:4804600-4814000	Weak transcription	Brain Substantia Nigra	brain
46	chr7:4804600-4814400	Weak transcription	Ovary	ovary
47	chr7:4804800-4812800	Weak transcription	HepG2	liver
48	chr7:4804800-4813800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr7:4805000-4813800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr7:4805000-4814000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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