Variant report

Variant	rs504350
Chromosome Location	chr19:56620260-56620261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56574744..56577085-chr19:56619874..56622339,2	K562	blood:
2	chr19:56618269..56620601-chr19:56650918..56652939,2	MCF-7	breast:
3	chr19:56617972..56620643-chr19:56620884..56623590,3	MCF-7	breast:
4	chr19:56617470..56621508-chr19:56630958..56634094,7	MCF-7	breast:
5	chr19:56619067..56621819-chr19:56683473..56686134,2	K562	blood:
6	chr19:56618895..56620681-chr19:56648201..56650740,2	K562	blood:

Variant related genes	Relation type
ENSG00000167685	Chromatin interaction
ENSG00000142409	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1007851	0.82[ASN][1000 genomes]
rs11673628	0.90[JPT][hapmap]
rs12459102	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12983086	0.89[CHD][hapmap];0.81[JPT][hapmap]
rs2450439	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2631625	0.81[ASN][1000 genomes]
rs2631627	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2631628	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2631631	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2631637	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2631640	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2637092	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2637094	0.83[ASN][1000 genomes]
rs2637097	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2637114	0.81[ASN][1000 genomes]
rs2932757	0.85[ASN][1000 genomes]
rs35766803	0.88[ASN][1000 genomes]
rs473953	0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs478402	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801676	0.89[CHD][hapmap];0.86[JPT][hapmap]
rs481936	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490345	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs492078	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497453	0.82[ASN][1000 genomes]
rs501798	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs506547	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs506782	0.94[EUR][1000 genomes]
rs509897	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs517021	0.90[AMR][1000 genomes]
rs517582	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521092	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs522980	0.81[AMR][1000 genomes]
rs524778	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs524829	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs524988	0.83[ASN][1000 genomes]
rs525827	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs526275	0.87[EUR][1000 genomes]
rs527715	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs530102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs533640	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs533734	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs535393	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536342	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs536414	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs537425	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540900	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]
rs547945	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs554681	1.00[EUR][1000 genomes]
rs564050	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564973	0.80[ASN][1000 genomes]
rs569310	0.81[ASN][1000 genomes]
rs570210	0.89[ASN][1000 genomes]
rs572851	0.86[ASN][1000 genomes]
rs578990	0.84[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs578991	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs582271	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs583330	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs588574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs592827	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs599405	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap]
rs604364	0.82[ASN][1000 genomes]
rs609736	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs609755	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs619934	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs626821	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs629544	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs630704	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs640654	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs642776	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs643133	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs643174	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs648352	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6509982	0.82[ASN][1000 genomes]
rs659424	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs662308	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs662763	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs665082	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs665846	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs665857	0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs667438	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667974	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs668056	1.00[EUR][1000 genomes]
rs669866	0.97[CHD][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap]
rs677127	0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs677142	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs678540	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs684653	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs685117	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7250351	0.82[ASN][1000 genomes]
rs8103672	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs9676765	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	esv1809307	chr19:56604027-56633623	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	esv1811581	chr19:56609313-56631618	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
18	esv1824038	chr19:56610449-56636632	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:56616000-56626600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr19:56616000-56627000	Enhancers	Liver	Liver
5	chr19:56616000-56627200	Enhancers	H1 Cell Line	embryonic stem cell
6	chr19:56616200-56620800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:56616600-56620400	Enhancers	Brain Hippocampus Middle	brain
8	chr19:56617200-56620400	Weak transcription	Primary T cells from cord blood	blood
9	chr19:56617200-56622000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr19:56617200-56622800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:56617200-56624400	Weak transcription	Hela-S3	cervix
12	chr19:56617200-56629200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:56617400-56620800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:56617400-56620800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr19:56617400-56621000	Genic enhancers	Lung	lung
16	chr19:56617400-56622400	Weak transcription	Fetal Brain Male	brain
17	chr19:56617400-56623400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:56617800-56620400	Genic enhancers	Pancreas	Pancrea
19	chr19:56618000-56621000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr19:56618200-56621000	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr19:56618200-56624400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:56618400-56622400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:56618400-56622400	Enhancers	Primary B cells from cord blood	blood
24	chr19:56618600-56620400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:56618600-56620400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:56618600-56620400	Strong transcription	Thymus	Thymus
27	chr19:56618600-56620600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:56618600-56621200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr19:56618600-56622000	Weak transcription	A549	lung
30	chr19:56618600-56622000	Weak transcription	K562	blood
31	chr19:56618600-56630000	Weak transcription	Dnd41	blood
32	chr19:56618800-56620800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:56618800-56621000	Enhancers	Psoas Muscle	Psoas
34	chr19:56618800-56621800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:56618800-56622800	Enhancers	Primary B cells from peripheral blood	blood
36	chr19:56618800-56622800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:56618800-56626400	Enhancers	Fetal Thymus	thymus
38	chr19:56619000-56620800	Enhancers	Small Intestine	intestine
39	chr19:56619000-56621800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:56619200-56620800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:56619200-56621000	Enhancers	Esophagus	oesophagus
42	chr19:56619200-56621000	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr19:56619200-56622200	Enhancers	Duodenum Mucosa	Duodenum
44	chr19:56619200-56624200	Enhancers	Placenta	Placenta
45	chr19:56619200-56627200	Enhancers	Left Ventricle	heart
46	chr19:56619400-56620600	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr19:56619400-56620800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:56619400-56621000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr19:56619400-56621000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:56619400-56621000	Enhancers	Brain Inferior Temporal Lobe	brain

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