Variant report

Variant	rs12334190
Chromosome Location	chr7:100894214-100894215
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:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100883935..100885996-chr7:100893008..100895659,3	K562	blood:
2	chr7:100858946..100862708-chr7:100892771..100897292,5	MCF-7	breast:
3	chr7:100859404..100861068-chr7:100894037..100896793,2	MCF-7	breast:
4	chr7:100883935..100886693-chr7:100893948..100895706,3	K562	blood:
5	chr7:100881101..100885645-chr7:100894081..100896862,4	MCF-7	breast:
6	chr7:100859409..100862433-chr7:100893851..100895703,4	K562	blood:
7	chr7:100878550..100881686-chr7:100893113..100895457,3	MCF-7	breast:
8	chr7:100893955..100895554-chr7:100940765..100942923,2	MCF-7	breast:
9	chr7:100860572..100862632-chr7:100892717..100896862,3	K562	blood:
10	chr7:100892265..100894287-chr7:100903598..100905585,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLDN15-1	chr7:100893301-100895582	NONHSAT122458

No data

Variant related genes	Relation type
ENSG00000106397	Chromatin interaction
ENSG00000214253	Chromatin interaction
ENSG00000106400	Chromatin interaction
ENSG00000232301	Chromatin interaction
ENSG00000106404	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10215699	0.95[EUR][1000 genomes]
rs10230349	0.82[AMR][1000 genomes]
rs10230367	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10241107	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10244139	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10252307	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10252506	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs10254892	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10255195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10257072	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10260707	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10260813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10265206	0.87[CEU][hapmap];0.82[GIH][hapmap]
rs10270498	0.85[EUR][1000 genomes]
rs10273837	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10487887	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12333955	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28535695	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28582264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28629340	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28673822	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28689891	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56749963	1.00[EUR][1000 genomes]
rs59554944	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59937851	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60536711	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60719606	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6946705	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6946706	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6947016	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6947521	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6947730	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6957526	0.95[EUR][1000 genomes]
rs6961873	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6964812	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6967483	0.87[CEU][hapmap];0.94[YRI][hapmap];0.95[EUR][1000 genomes]
rs6975417	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979122	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs6979308	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979710	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979867	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73713820	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73713821	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73713822	0.88[AFR][1000 genomes]
rs7778271	0.80[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[EUR][1000 genomes]
rs7808669	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
11	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
12	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
13	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
14	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
15	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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs12334190	CLDN15	cis	Thyroid	GTEx
rs12334190	FIS1	cis	lung	GTEx
rs12334190	CLDN15	cis	Skin Sun Exposed Lower leg	GTEx
rs12334190	FIS1	cis	Stomach	GTEx
rs12334190	FIS1	cis	Adipose Subcutaneous	GTEx
rs12334190	FIS1	cis	Esophagus Muscularis	GTEx
rs12334190	FIS1	cis	Esophagus Mucosa	GTEx
rs12334190	CLDN15	cis	multi-tissue	Pritchard
rs12334190	FIS1	cis	Whole Blood	GTEx
rs12334190	FIS1	cis	lymphoblastoid	seeQTL
rs12334190	FIS1	cis	Thyroid	GTEx
rs12334190	FIS1	cis	Artery Aorta	GTEx
rs12334190	FIS1	cis	Artery Tibial	GTEx
rs12334190	CLDN15	cis	Esophagus Muscularis	GTEx
rs12334190	FIS1	cis	Heart Left Ventricle	GTEx
rs12334190	FIS1	Cis_1M	lymphoblastoid	RTeQTL
rs12334190	CLDN15	Cis_1M	lymphoblastoid	RTeQTL
rs12334190	CLDN15	cis	Whole Blood	GTEx
rs12334190	FIS1	cis	Skin Sun Exposed Lower leg	GTEx
rs12334190	CLDN15	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100888800-100894600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:100888800-100894600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:100888800-100894600	Weak transcription	Aorta	Aorta
4	chr7:100888800-100894600	Weak transcription	Esophagus	oesophagus
5	chr7:100888800-100894600	Weak transcription	Fetal Kidney	kidney
6	chr7:100889000-100894400	Weak transcription	HSMM	muscle
7	chr7:100889000-100894600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:100889000-100894600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:100889000-100894600	Weak transcription	HSMMtube	muscle
10	chr7:100889000-100894600	Weak transcription	NH-A	brain
11	chr7:100889200-100894400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:100889200-100894600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:100889400-100894400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr7:100889400-100894400	Weak transcription	Small Intestine	intestine
15	chr7:100889400-100894400	Weak transcription	A549	lung
16	chr7:100889400-100894600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:100889400-100894600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:100889400-100894600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:100889600-100894600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:100889600-100894600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:100890400-100894400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:100892400-100894600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:100892800-100894400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr7:100892800-100894600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:100893000-100894600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr7:100893200-100894400	Enhancers	Fetal Brain Male	brain
27	chr7:100893400-100894400	Enhancers	Primary T cells from cord blood	blood
28	chr7:100893400-100894400	Genic enhancers	Fetal Thymus	thymus
29	chr7:100893400-100894600	Enhancers	Primary B cells from cord blood	blood
30	chr7:100893400-100894600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr7:100893400-100894600	Enhancers	Brain Cingulate Gyrus	brain
32	chr7:100893600-100894400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:100893600-100894400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr7:100893600-100894400	Enhancers	Primary hematopoietic stem cells	blood
35	chr7:100893600-100894400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:100893600-100894400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:100893600-100894400	Enhancers	Duodenum Mucosa	Duodenum
38	chr7:100893600-100894400	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr7:100893600-100894400	Enhancers	HUVEC	blood vessel
40	chr7:100893600-100894400	Enhancers	NHDF-Ad	bronchial
41	chr7:100893600-100894400	Genic enhancers	NHEK	skin
42	chr7:100893600-100894600	Enhancers	Primary B cells from peripheral blood	blood
43	chr7:100893600-100894600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr7:100893600-100894600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr7:100893600-100894600	Enhancers	Liver	Liver
46	chr7:100893600-100894600	Enhancers	Brain Hippocampus Middle	brain
47	chr7:100893600-100894600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr7:100893600-100894600	Enhancers	Fetal Lung	lung
49	chr7:100893600-100894600	Genic enhancers	Fetal Stomach	stomach
50	chr7:100893600-100894600	Enhancers	Skeletal Muscle Female	skeletal muscle

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