Variant report

Variant	rs7247515
Chromosome Location	chr19:40755915-40755916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40752594..40756116-chr19:40758257..40762594,4	K562	blood:
2	chr19:40753793..40756540-chr19:40760904..40762760,3	K562	blood:
3	chr19:40732755..40733312-chr19:40755398..40756094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11666690	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11667443	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11668006	0.88[CEU][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes]
rs11668520	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11669006	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11669332	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11670323	0.81[AMR][1000 genomes]
rs11670860	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670912	0.86[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11671439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17846842	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356230	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28746190	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35090721	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36058450	0.92[ASN][1000 genomes]
rs3730052	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730055	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730262	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3760636	0.85[CHB][hapmap]
rs41275746	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275748	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275750	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45497695	0.83[EUR][1000 genomes]
rs56672337	0.83[EUR][1000 genomes]
rs58094119	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59058760	0.83[EUR][1000 genomes]
rs59106111	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6508937	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes]
rs66623822	0.83[EUR][1000 genomes]
rs67587726	0.83[EUR][1000 genomes]
rs7252506	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73933218	0.92[ASN][1000 genomes]
rs73933225	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933232	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933236	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933237	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933238	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933240	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73933241	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8105478	0.86[AMR][1000 genomes]
rs873143	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs874269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS 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	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1062755	chr19:40737463-40758235	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv1059094	chr19:40745377-40758235	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7247515	C19orf47	cis	lymphoblastoid	seeQTL
rs7247515	HSD17B14	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40732800-40759000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:40735600-40757600	Weak transcription	Stomach Mucosa	stomach
3	chr19:40738000-40763800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr19:40738200-40756200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr19:40738800-40758000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:40739200-40758400	Strong transcription	Fetal Intestine Small	intestine
7	chr19:40741600-40761000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:40743200-40760800	Weak transcription	HMEC	breast
9	chr19:40745800-40760800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:40746400-40760800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:40746600-40758000	Weak transcription	K562	blood
12	chr19:40747200-40759400	Weak transcription	Hela-S3	cervix
13	chr19:40747200-40760800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:40747400-40757600	Weak transcription	HSMM	muscle
15	chr19:40747400-40759200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:40747600-40757400	Weak transcription	Primary B cells from cord blood	blood
17	chr19:40748200-40757600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:40748200-40758200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:40748400-40758400	Weak transcription	Osteobl	bone
20	chr19:40748400-40761000	Weak transcription	Small Intestine	intestine
21	chr19:40748600-40758000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr19:40748600-40759400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:40748800-40758000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:40748800-40758000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:40748800-40760800	Weak transcription	NH-A	brain
26	chr19:40749000-40759000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:40749400-40759200	Weak transcription	HUVEC	blood vessel
28	chr19:40750000-40763800	Strong transcription	Thymus	Thymus
29	chr19:40750000-40764000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr19:40750600-40756000	Genic enhancers	Spleen	Spleen
31	chr19:40750600-40756200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr19:40751000-40761800	Weak transcription	Fetal Kidney	kidney
33	chr19:40751200-40758600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:40751200-40761600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:40751200-40771200	Weak transcription	Fetal Heart	heart
36	chr19:40751600-40758000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr19:40751600-40758400	Weak transcription	HSMMtube	muscle
38	chr19:40751800-40757800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:40751800-40758400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:40751800-40763600	Strong transcription	Fetal Stomach	stomach
41	chr19:40752000-40757600	Weak transcription	Ovary	ovary
42	chr19:40752000-40759000	Weak transcription	NHDF-Ad	bronchial
43	chr19:40752400-40756000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr19:40752600-40756000	Genic enhancers	Fetal Muscle Trunk	muscle
45	chr19:40752600-40756800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr19:40752600-40757000	Strong transcription	Fetal Intestine Large	intestine
47	chr19:40752600-40763400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:40752800-40758400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:40752800-40763400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:40753000-40756000	Genic enhancers	Pancreas	Pancrea

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