Variant report

Variant	rs7253691
Chromosome Location	chr19:42403607-42403608
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42400409..42404033-chr19:42410840..42416491,6	K562	blood:
2	chr19:42403036..42406958-chr19:42407264..42409613,3	MCF-7	breast:
3	chr19:42397636..42399907-chr19:42401318..42404591,3	K562	blood:
4	chr19:42392300..42393961-chr19:42403075..42405096,2	K562	blood:
5	chr19:42388132..42389933-chr19:42401964..42404218,2	K562	blood:

Variant related genes	Relation type
ENSG00000076928	Chromatin interaction
ENSG00000268041	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10401189	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10401937	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10402667	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10403081	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10414811	1.00[CEU][hapmap]
rs10417495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10419314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083638	1.00[CEU][hapmap]
rs11083640	1.00[CEU][hapmap]
rs11878536	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs11878555	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap]
rs11878734	1.00[CEU][hapmap]
rs11878811	1.00[CEU][hapmap]
rs11879437	1.00[CEU][hapmap]
rs11880977	1.00[CEU][hapmap]
rs11881323	1.00[CEU][hapmap]
rs11883018	1.00[CEU][hapmap]
rs12104228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs16975619	0.94[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288509	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs2288510	0.94[ASN][1000 genomes]
rs2288511	0.94[ASN][1000 genomes]
rs2288512	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303798	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs28396197	0.86[AMR][1000 genomes]
rs28521795	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs28706300	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745222	0.97[CHD][hapmap];0.91[JPT][hapmap]
rs6509003	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs717225	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7252790	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252800	0.91[ASN][1000 genomes]
rs7260129	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs73550603	0.94[ASN][1000 genomes]
rs73550610	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73550618	1.00[EUR][1000 genomes]
rs8109784	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109959	0.91[ASN][1000 genomes]
rs8110305	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs8113339	1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs8113686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs891169	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs891170	0.94[ASN][1000 genomes]
rs891171	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs891172	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9653098	1.00[CEU][hapmap]
rs9989667	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription 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 miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
9	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv579625	chr19:42400893-42406507	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42389200-42407200	Weak transcription	Fetal Kidney	kidney
2	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
3	chr19:42389400-42406000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:42389400-42411400	Weak transcription	Fetal Brain Male	brain
5	chr19:42389800-42409000	Strong transcription	Fetal Stomach	stomach
6	chr19:42390800-42411200	Weak transcription	Hela-S3	cervix
7	chr19:42391400-42407400	Weak transcription	K562	blood
8	chr19:42391600-42404600	Weak transcription	HSMM	muscle
9	chr19:42392000-42404000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:42392000-42412600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr19:42392000-42412600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:42392000-42412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:42392200-42407600	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:42392200-42408400	Strong transcription	Liver	Liver
15	chr19:42392200-42412400	Strong transcription	Fetal Muscle Leg	muscle
16	chr19:42392200-42412800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr19:42392400-42407600	Strong transcription	Fetal Intestine Small	intestine
18	chr19:42392400-42410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:42392400-42412400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:42392400-42413200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:42392600-42406200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:42392600-42407400	Strong transcription	Colonic Mucosa	Colon
23	chr19:42392600-42411800	Strong transcription	Placenta	Placenta
24	chr19:42392600-42413600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr19:42392800-42407800	Strong transcription	Fetal Intestine Large	intestine
26	chr19:42393400-42404600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr19:42393400-42413600	Strong transcription	Thymus	Thymus
28	chr19:42393800-42404400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:42393800-42413000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:42394000-42413000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:42394800-42405000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:42395600-42412400	Strong transcription	Right Ventricle	heart
33	chr19:42395800-42407400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr19:42395800-42407600	Strong transcription	NHLF	lung
35	chr19:42395800-42411600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr19:42395800-42411800	Strong transcription	Fetal Brain Female	brain
37	chr19:42396000-42407000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:42396000-42408800	Strong transcription	Rectal Smooth Muscle	rectum
39	chr19:42396000-42411800	Strong transcription	Brain Hippocampus Middle	brain
40	chr19:42396000-42412000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr19:42396800-42415200	Strong transcription	Dnd41	blood
42	chr19:42397000-42406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:42397000-42408200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:42397400-42404800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr19:42397400-42411600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:42397400-42413600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:42397600-42412800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr19:42398000-42411200	Strong transcription	Primary B cells from cord blood	blood
49	chr19:42398000-42411400	Strong transcription	Aorta	Aorta
50	chr19:42398000-42411400	Strong transcription	Esophagus	oesophagus

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