Variant report

Variant	rs540900
Chromosome Location	chr19:56602374-56602375
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56601536..56604040-chr19:56606734..56609466,2	MCF-7	breast:
2	chr19:56600333..56603154-chr19:56649687..56651196,2	K562	blood:
3	chr19:56599644..56602994-chr19:56620278..56624249,5	K562	blood:
4	chr19:56600362..56602994-chr19:56622256..56625120,2	K562	blood:
5	chr19:56601293..56604131-chr19:56623089..56625582,2	MCF-7	breast:
6	chr19:56592253..56593839-chr19:56602016..56603722,2	K562	blood:
7	chr19:56601141..56604014-chr19:56651251..56654882,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167685	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1007851	0.84[ASN][1000 genomes]
rs11673628	0.86[JPT][hapmap]
rs12459102	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12983086	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs2631627	0.81[AMR][1000 genomes]
rs2631631	1.00[CEU][hapmap]
rs2631637	0.88[EUR][1000 genomes]
rs2631640	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2637092	0.84[JPT][hapmap]
rs473953	0.90[JPT][hapmap]
rs478402	0.88[EUR][1000 genomes]
rs4801676	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs481936	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs490345	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs492078	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs501798	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs504350	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506547	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap]
rs506782	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs509897	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs517582	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs521092	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs524778	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs524829	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs525827	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap]
rs526275	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs530102	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs533640	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs533734	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs535393	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs536342	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs536414	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs537425	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs547945	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs554681	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs564050	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs570210	0.91[ASN][1000 genomes]
rs578990	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs578991	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap]
rs582271	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs588574	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs592827	0.88[EUR][1000 genomes]
rs599405	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs604364	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs609736	1.00[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs619934	1.00[ASW][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs626821	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap]
rs629544	1.00[CEU][hapmap]
rs630704	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs642776	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs643133	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap]
rs648352	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6509982	0.84[ASN][1000 genomes]
rs659424	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap]
rs662308	0.81[EUR][1000 genomes]
rs662763	0.81[EUR][1000 genomes]
rs665082	0.81[EUR][1000 genomes]
rs665846	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs665857	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs667438	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs667974	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs668056	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs669866	0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap]
rs677127	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs677142	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs678540	0.81[EUR][1000 genomes]
rs684653	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs685117	1.00[CEU][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs7250351	0.85[ASN][1000 genomes]
rs8103672	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs9676765	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1062406	chr19:56382492-56602374	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1058988	chr19:56382492-56609032	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
5	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
6	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
7	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS 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	41 gene(s)	inside rSNPs	diseases
8	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
10	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
11	nsv912512	chr19:56592286-56636759	Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
13	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
15	nsv912514	chr19:56596815-56636759	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
16	nsv912515	chr19:56598829-56623710	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
17	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56592600-56620000	Weak transcription	HSMMtube	muscle
2	chr19:56592800-56602400	Weak transcription	Brain Anterior Caudate	brain
3	chr19:56592800-56602800	Weak transcription	Right Atrium	heart
4	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:56593000-56602400	Weak transcription	Osteobl	bone
6	chr19:56593000-56606400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr19:56593000-56616200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:56593000-56616600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:56593000-56616800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:56593600-56616000	Weak transcription	Stomach Mucosa	stomach
12	chr19:56594800-56616800	Weak transcription	HUVEC	blood vessel
13	chr19:56596200-56603400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:56596400-56605400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:56596600-56602800	Strong transcription	Fetal Stomach	stomach
16	chr19:56596600-56603600	Strong transcription	Fetal Intestine Small	intestine
17	chr19:56596600-56604000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:56596600-56604200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:56596600-56604400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:56596600-56604600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:56596600-56614800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:56596800-56603000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr19:56597000-56602600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr19:56597000-56603600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:56597000-56604000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:56597200-56602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:56597200-56619400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:56597800-56604000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr19:56598000-56604000	Weak transcription	GM12878-XiMat	blood
30	chr19:56598000-56605400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:56598200-56604800	Strong transcription	Gastric	stomach
32	chr19:56598600-56603200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:56598800-56602800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr19:56598800-56603200	Strong transcription	Fetal Intestine Large	intestine
35	chr19:56598800-56604600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:56599800-56602800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:56599800-56605400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr19:56599800-56615200	Strong transcription	Liver	Liver
39	chr19:56600000-56603000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr19:56600000-56603000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr19:56600000-56603000	Strong transcription	Dnd41	blood
42	chr19:56600000-56603200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr19:56600000-56603600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:56600000-56604000	Strong transcription	Fetal Muscle Leg	muscle
45	chr19:56600000-56604200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:56600000-56604600	Strong transcription	Primary T cells from cord blood	blood
47	chr19:56600000-56619000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:56600200-56602600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:56600400-56602400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:56600400-56602400	Strong transcription	Thymus	Thymus

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