Variant report

Variant	rs273512
Chromosome Location	chr19:18224729-18224730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18222417..18225147-chr19:18278343..18280601,2	K562	blood:
2	chr19:18223413..18225267-chr19:18389021..18391701,2	MCF-7	breast:
3	chr19:18223254..18225164-chr19:18359202..18360935,2	MCF-7	breast:
4	chr19:18221370..18225570-chr19:18281074..18286554,5	K562	blood:
5	chr19:18215138..18216766-chr19:18223836..18225347,2	MCF-7	breast:
6	chr19:18223237..18224925-chr19:18271250..18272997,12	MCF-7	breast:
7	chr19:18223950..18226906-chr19:18227194..18230547,6	K562	blood:

Variant related genes	Relation type
ENSG00000216490	Chromatin interaction
ENSG00000105647	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11086089	0.83[EUR][1000 genomes]
rs11665905	0.83[EUR][1000 genomes]
rs11667917	0.81[EUR][1000 genomes]
rs11669624	0.84[JPT][hapmap]
rs11670228	0.82[EUR][1000 genomes]
rs11673702	0.82[EUR][1000 genomes]
rs12052085	0.83[EUR][1000 genomes]
rs2173006	0.83[EUR][1000 genomes]
rs273496	1.00[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs273503	0.87[EUR][1000 genomes]
rs273504	0.83[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs273505	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs273506	0.83[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs273507	0.88[AFR][1000 genomes]
rs273508	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs273510	0.85[AFR][1000 genomes]
rs3730179	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs4808746	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56971820	0.83[EUR][1000 genomes]
rs58049250	0.82[EUR][1000 genomes]
rs62121155	0.83[EUR][1000 genomes]
rs62121158	0.84[EUR][1000 genomes]
rs62123561	0.81[ASN][1000 genomes]
rs62123609	0.82[EUR][1000 genomes]
rs7249862	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	nsv470130	chr19:18047283-18234587	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription 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	147 gene(s)	inside rSNPs	diseases
6	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv911243	chr19:18206681-18283501	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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 target site	37 gene(s)	inside rSNPs	diseases
12	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
14	esv1834142	chr19:18224729-18234588	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
15	nsv911246	chr19:18224729-18283501	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv911247	chr19:18224729-18288069	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
19	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
20	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription 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	136 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs273512	ZNF714	cis	parietal	SCAN
rs273512	HAPLN4	cis	cerebellum	SCAN
rs273512	TM6SF2	cis	cerebellum	SCAN
rs273512	KLHL26	cis	cerebellum	SCAN
rs273512	HSH2D	cis	cerebellum	SCAN
rs273512	ANKLE1	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18221600-18226000	Weak transcription	Aorta	Aorta
2	chr19:18221600-18228000	Weak transcription	Ovary	ovary
3	chr19:18221600-18228200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:18221600-18228200	Weak transcription	Left Ventricle	heart
5	chr19:18221800-18226000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr19:18221800-18226400	Weak transcription	Osteobl	bone
7	chr19:18221800-18227800	Weak transcription	Colon Smooth Muscle	Colon
8	chr19:18221800-18228000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:18221800-18228000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:18221800-18228000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:18221800-18228200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:18221800-18228200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:18221800-18228200	Weak transcription	Right Atrium	heart
14	chr19:18221800-18228200	Weak transcription	HMEC	breast
15	chr19:18221800-18228200	Weak transcription	NHLF	lung
16	chr19:18221800-18228400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:18222000-18225200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:18222000-18225400	Weak transcription	Gastric	stomach
19	chr19:18222000-18228000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:18222000-18228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:18222000-18228200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:18222000-18228200	Weak transcription	Right Ventricle	heart
23	chr19:18222000-18228200	Weak transcription	NHDF-Ad	bronchial
24	chr19:18222200-18225400	Weak transcription	Adipose Nuclei	Adipose
25	chr19:18222200-18225400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:18222200-18227800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr19:18222200-18227800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:18222200-18227800	Weak transcription	Thymus	Thymus
29	chr19:18222200-18228000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:18222400-18225000	Genic enhancers	Monocytes-CD14+_RO01746	blood
31	chr19:18222400-18228000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr19:18222400-18228000	Weak transcription	Stomach Mucosa	stomach
33	chr19:18222600-18228000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr19:18223000-18226000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:18223000-18228200	Weak transcription	HSMMtube	muscle
36	chr19:18223200-18225600	Weak transcription	Fetal Stomach	stomach
37	chr19:18223400-18225400	Weak transcription	Brain Anterior Caudate	brain
38	chr19:18223600-18224800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr19:18223600-18225000	Genic enhancers	Fetal Intestine Small	intestine
40	chr19:18223800-18225800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:18223800-18226800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:18224000-18225600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:18224000-18226400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:18224000-18227800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:18224000-18227800	Weak transcription	Placenta	Placenta
46	chr19:18224000-18227800	Weak transcription	Fetal Thymus	thymus
47	chr19:18224000-18227800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:18224000-18227800	Weak transcription	Hela-S3	cervix
49	chr19:18224000-18227800	Weak transcription	K562	blood
50	chr19:18224000-18228000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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