Variant report

Variant	rs3757460
Chromosome Location	chr7:100881640-100881641
allele	A/G
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	chr7:100881384-100884442	K562	blood:	n/a	n/a
2	POLR2A	chr7:100880736-100882068	K562	blood:	n/a	n/a
3	MAZ	chr7:100880667-100882489	IMR90	lung:	n/a	chr7:100881200-100881210 chr7:100881158-100881168 chr7:100881196-100881206
4	POLR2A	chr7:100880765-100882134	HepG2	liver:	n/a	n/a
5	POLR2A	chr7:100880613-100882236	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100858977..100861910-chr7:100881462..100883229,2	K562	blood:
2	chr7:100859877..100865511-chr7:100878168..100882490,7	MCF-7	breast:
3	chr7:100881101..100885645-chr7:100894081..100896862,4	MCF-7	breast:
4	chr7:100858331..100862020-chr7:100880126..100882464,3	K562	blood:
5	chr7:100878550..100881686-chr7:100893113..100895457,3	MCF-7	breast:

Variant related genes	Relation type
CLDN15	TF binding region
ENSG00000106397	Chromatin interaction
ENSG00000106400	Chromatin interaction
ENSG00000214253	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10250685	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047319	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs1056678	0.91[ASN][1000 genomes]
rs10953329	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10953330	0.95[ASN][1000 genomes]
rs11769624	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11977597	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs17319250	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2072168	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.94[ASN][1000 genomes]
rs2074685	0.94[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2302428	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28361887	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35082269	0.96[ASN][1000 genomes]
rs35094522	0.94[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35550811	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3757459	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757462	0.84[CEU][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes]
rs3807511	0.84[CEU][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes]
rs4729672	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4729673	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4729676	0.80[EUR][1000 genomes]
rs62482972	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv2422376	chr7:100743485-101016471	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv534186	chr7:100773842-100898909	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv464651	chr7:100792810-100971604	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv607974	chr7:100792810-100971604	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv429788	chr7:100799565-101178565	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	esv2752134	chr7:100800131-101141867	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv464652	chr7:100804140-100881640	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv607976	chr7:100804140-100881640	Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv888817	chr7:100804140-100881640	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv607977	chr7:100818846-100881640	Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
14	nsv831076	chr7:100828847-101011674	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
15	nsv888818	chr7:100833153-100895480	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
16	nsv888819	chr7:100833153-100920007	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
17	esv2422326	chr7:100833449-101000131	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv607978	chr7:100861213-100971604	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
19	nsv831077	chr7:100874209-101083930	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3757460	CLDN15	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100862400-100887000	Weak transcription	Fetal Kidney	kidney
2	chr7:100863800-100884000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:100863800-100886800	Weak transcription	Psoas Muscle	Psoas
4	chr7:100863800-100886800	Weak transcription	Hela-S3	cervix
5	chr7:100865000-100884800	Strong transcription	Thymus	Thymus
6	chr7:100868400-100887600	Weak transcription	Small Intestine	intestine
7	chr7:100868800-100884200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:100872200-100881800	Weak transcription	Primary B cells from cord blood	blood
9	chr7:100876000-100887000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:100876200-100883800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:100876200-100884400	Weak transcription	HMEC	breast
12	chr7:100876400-100883000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:100876400-100887000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:100876600-100881800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:100876800-100881800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:100876800-100883200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr7:100876800-100883200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr7:100876800-100886800	Weak transcription	Fetal Brain Male	brain
19	chr7:100877200-100884400	Strong transcription	Fetal Brain Female	brain
20	chr7:100877400-100884600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:100877600-100882600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:100878000-100882800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:100878000-100884600	Genic enhancers	Spleen	Spleen
24	chr7:100878200-100884600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:100878200-100885000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr7:100878400-100881800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
27	chr7:100878400-100882200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr7:100878400-100883000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:100878400-100884000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:100878400-100884400	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr7:100878600-100881800	Weak transcription	K562	blood
32	chr7:100878600-100883000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:100878600-100884800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr7:100878800-100882600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:100878800-100884200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr7:100879000-100883000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:100879000-100884200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr7:100879000-100884600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr7:100879200-100883800	Strong transcription	Esophagus	oesophagus
40	chr7:100879200-100884400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:100879200-100884600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:100879400-100883000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
43	chr7:100879600-100882400	Genic enhancers	Lung	lung
44	chr7:100879600-100883000	Strong transcription	Gastric	stomach
45	chr7:100879600-100884600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:100879600-100884600	Strong transcription	Brain Germinal Matrix	brain
47	chr7:100879800-100884200	Strong transcription	Dnd41	blood
48	chr7:100880000-100882200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:100880000-100882600	Weak transcription	Primary T cells from cord blood	blood
50	chr7:100880000-100882600	Enhancers	Placenta Amnion	Placenta Amnion

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