Variant report

Variant	rs1197669
Chromosome Location	chr15:42138456-42138457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42136531..42140635-chr15:42140718..42144467,4	MCF-7	breast:
2	chr15:42119559..42121524-chr15:42137744..42139506,3	K562	blood:
3	chr15:42128850..42133555-chr15:42135364..42139036,5	K562	blood:

Variant related genes	Relation type
ENSG00000137877	Chromatin interaction
ENSG00000168970	Chromatin interaction
ENSG00000250379	Chromatin interaction
ENSG00000200293	Chromatin interaction
ENSG00000243789	Chromatin interaction
ENSG00000243708	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1122884	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630972	0.91[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs11631051	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632519	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633160	1.00[ASN][1000 genomes]
rs11634083	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634804	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11636523	0.82[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs1197660	0.87[CEU][hapmap]
rs1197667	0.88[CEU][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1197671	0.83[ASW][hapmap];0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs1197672	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1197702	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1197703	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1197705	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1197706	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1201689	0.81[CEU][hapmap]
rs12906666	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12917387	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs17677098	0.91[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]
rs17677757	0.87[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs17678310	0.83[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs2178003	0.91[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs2925339	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs34621600	1.00[ASN][1000 genomes]
rs35476790	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923917	0.80[YRI][hapmap]
rs7167078	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs8025614	0.80[YRI][hapmap]
rs8042809	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs890497	0.84[AFR][1000 genomes]
rs890503	0.90[TSI][hapmap]
rs9646193	0.91[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS 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	45 gene(s)	inside rSNPs	diseases
3	nsv904115	chr15:42076387-42171483	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1038393	chr15:42083574-42188035	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
6	esv1827003	chr15:42087505-42199076	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816120	chr15:42093384-42171578	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases
8	nsv1041645	chr15:42095168-42186482	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1051200	chr15:42095168-42188035	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
10	nsv517631	chr15:42096926-42187492	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1051733	chr15:42098896-42186482	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
12	nsv1036153	chr15:42098896-42188035	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer 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	38 gene(s)	inside rSNPs	diseases
14	nsv1048606	chr15:42101694-42192760	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
15	nsv904117	chr15:42103822-42184794	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
16	nsv904118	chr15:42103822-42207905	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
17	nsv904119	chr15:42109975-42142912	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv904120	chr15:42109975-42153085	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	nsv904121	chr15:42109975-42162957	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
20	nsv904122	chr15:42109975-42166475	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
21	nsv904123	chr15:42109975-42171483	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
22	nsv904124	chr15:42109975-42207905	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
23	nsv9244	chr15:42110712-42208805	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
24	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
25	nsv1050892	chr15:42128855-42186482	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
26	nsv904126	chr15:42132896-42171483	Enhancers Strong transcription Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
27	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS 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	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1197669	EHD4	cis	multi-tissue	Pritchard
rs1197669	MAPKBP1	cis	multi-tissue	Pritchard
rs1197669	NDUFAF1	cis	parietal	SCAN
rs1197669	CAPN3	cis	parietal	SCAN
rs1197669	SNAP23	cis	parietal	SCAN
rs1197669	SPTBN5	cis	Artery Tibial	GTEx
rs1197669	MAPKBP1	cis	cerebellum	SCAN
rs1197669	RPAP1	cis	parietal	SCAN
rs1197669	SPTBN5	cis	cerebellum	SCAN
rs1197669	MAPKBP1	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42121000-42147400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:42121400-42147600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:42121400-42147600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:42121600-42138600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:42121600-42141400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:42121600-42141800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:42121800-42140400	Weak transcription	Hela-S3	cervix
8	chr15:42122000-42142400	Strong transcription	Fetal Stomach	stomach
9	chr15:42122000-42142600	Strong transcription	Fetal Intestine Small	intestine
10	chr15:42122200-42145400	Weak transcription	HepG2	liver
11	chr15:42122400-42142600	Weak transcription	Fetal Brain Male	brain
12	chr15:42124200-42142400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:42125400-42142200	Weak transcription	GM12878-XiMat	blood
14	chr15:42125600-42142400	Weak transcription	Dnd41	blood
15	chr15:42126200-42142000	Strong transcription	Primary T cells from cord blood	blood
16	chr15:42126200-42152400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr15:42126600-42140400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:42126800-42141600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:42127000-42141600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:42127000-42143600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:42128200-42141600	Strong transcription	Fetal Intestine Large	intestine
22	chr15:42128600-42138800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:42128600-42139800	Weak transcription	HUVEC	blood vessel
24	chr15:42128600-42141200	Strong transcription	Ovary	ovary
25	chr15:42130400-42138800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr15:42131000-42140400	Weak transcription	HMEC	breast
27	chr15:42131000-42162800	Weak transcription	HSMM	muscle
28	chr15:42131200-42141000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:42131800-42138600	Weak transcription	Stomach Mucosa	stomach
30	chr15:42131800-42141000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:42131800-42141400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr15:42131800-42142600	Weak transcription	Psoas Muscle	Psoas
33	chr15:42132000-42141200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:42132000-42141800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:42132200-42141400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr15:42132200-42141600	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr15:42132200-42141600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:42132200-42141800	Strong transcription	Brain Germinal Matrix	brain
39	chr15:42132200-42143400	Strong transcription	Fetal Muscle Leg	muscle
40	chr15:42132400-42141400	Strong transcription	Brain Angular Gyrus	brain
41	chr15:42132400-42141600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:42132400-42141600	Strong transcription	Pancreas	Pancrea
43	chr15:42132400-42141800	Strong transcription	Thymus	Thymus
44	chr15:42132600-42141000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:42132600-42141200	Strong transcription	Lung	lung
46	chr15:42132600-42141400	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr15:42132600-42141400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr15:42132600-42141600	Strong transcription	Brain Hippocampus Middle	brain
49	chr15:42132600-42141800	Strong transcription	Liver	Liver
50	chr15:42132600-42141800	Strong transcription	Gastric	stomach

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