Variant report

Variant	rs669866
Chromosome Location	chr19:56651323-56651324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr19:56651051-56652992	K562	blood:	n/a	chr19:56652098-56652107 chr19:56651439-56651449 chr19:56651439-56651449 chr19:56651439-56651449 chr19:56651439-56651449
2	POLR2A	chr19:56651244-56652769	GM12891	blood:	n/a	n/a
3	E2F6	chr19:56651108-56651521	K562	blood:	n/a	n/a
4	MAX	chr19:56651115-56652766	K562	blood:	n/a	chr19:56652454-56652463 chr19:56652551-56652561 chr19:56652456-56652463
5	TEAD4	chr19:56651228-56651887	K562	blood:	n/a	n/a
6	POLR2A	chr19:56651273-56653019	K562	blood:	n/a	n/a
7	E2F6	chr19:56651242-56651487	K562	blood:	n/a	n/a
8	MAX	chr19:56651243-56651486	K562	blood:	n/a	n/a
9	E2F6	chr19:56651279-56652655	K562	blood:	n/a	chr19:56652629-56652636 chr19:56652628-56652636 chr19:56652514-56652525

No.	Distal block	Cell Line	Cell type
1	chr19:56629015..56635457-chr19:56649954..56657591,25	MCF-7	breast:
2	chr19:56629593..56635165-chr19:56650391..56656450,20	K562	blood:
3	chr19:56650990..56653515-chr19:56668518..56670798,3	K562	blood:
4	chr17:59476094..59477782-chr19:56651036..56652718,2	MCF-7	breast:
5	chr19:56627257..56634581-chr19:56650310..56656612,28	MCF-7	breast:
6	chr19:56650916..56653050-chr19:56823772..56825517,2	K562	blood:
7	chr19:56629593..56636020-chr19:56650029..56654099,17	K562	blood:

Variant related genes	Relation type
ZNF444	TF binding region
ENSG00000267131	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000267298	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000267280	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11673628	0.85[JPT][hapmap]
rs12983086	0.85[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2450439	0.90[ASN][1000 genomes]
rs2631625	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631627	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631628	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631631	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631637	0.86[ASN][1000 genomes]
rs2631640	0.81[ASN][1000 genomes]
rs2637088	0.81[ASN][1000 genomes]
rs2637092	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2637094	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2637097	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2637114	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932757	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs473953	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs478402	0.86[ASN][1000 genomes]
rs4801294	0.80[ASN][1000 genomes]
rs4801676	0.86[CHD][hapmap];0.91[JPT][hapmap]
rs490345	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs497453	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs504350	0.97[CHD][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap]
rs506547	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs517021	0.85[ASN][1000 genomes]
rs522980	0.83[AMR][1000 genomes]
rs524778	0.83[ASN][1000 genomes]
rs524829	0.83[ASN][1000 genomes]
rs524988	0.85[ASN][1000 genomes]
rs525827	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs527715	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs540900	0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap]
rs544365	0.82[ASN][1000 genomes]
rs545570	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs547002	0.81[ASN][1000 genomes]
rs547945	0.85[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs569310	0.82[ASN][1000 genomes]
rs572851	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs578990	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs578991	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs583330	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs587702	0.80[ASN][1000 genomes]
rs588574	0.90[JPT][hapmap]
rs592827	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs599405	0.80[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs609736	0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap]
rs619934	0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs626821	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs629544	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs640654	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs643133	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs643174	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs659424	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs662308	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs662763	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs665082	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs665857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs667438	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs667523	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs667974	0.83[ASN][1000 genomes]
rs677127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs678540	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs684653	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs685117	0.89[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap]
rs8103672	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs9676765	0.85[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv528361	chr19:56638845-56688570	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56638800-56651800	Weak transcription	Spleen	Spleen
2	chr19:56644200-56651400	Weak transcription	Right Atrium	heart
3	chr19:56645400-56651800	Enhancers	Pancreas	Pancrea
4	chr19:56645800-56651400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:56645800-56651600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:56646000-56651400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:56646000-56651600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:56646000-56651600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:56646800-56651600	Enhancers	Liver	Liver
10	chr19:56647000-56651400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:56648000-56651400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:56648000-56651400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:56648000-56651600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr19:56648200-56651400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:56648800-56651600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr19:56649000-56651400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr19:56649000-56651600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr19:56649000-56652000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr19:56649200-56651400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:56649200-56651400	Weak transcription	Colonic Mucosa	Colon
21	chr19:56649200-56651600	Weak transcription	Esophagus	oesophagus
22	chr19:56649400-56651400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:56650400-56651400	Enhancers	Primary B cells from cord blood	blood
24	chr19:56650400-56651400	Weak transcription	Stomach Mucosa	stomach
25	chr19:56650600-56651800	Enhancers	Gastric	stomach
26	chr19:56650800-56651400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:56650800-56651400	Enhancers	Thymus	Thymus
28	chr19:56651000-56651400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr19:56651200-56651400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:56651200-56651400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:56651200-56651400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr19:56651200-56651400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr19:56651200-56651400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr19:56651200-56651400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:56651200-56651400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr19:56651200-56651400	Enhancers	Primary B cells from peripheral blood	blood
37	chr19:56651200-56651400	Enhancers	Primary T cells from cord blood	blood
38	chr19:56651200-56651400	Enhancers	Primary T cells fromperipheralblood	blood
39	chr19:56651200-56651400	Enhancers	Primary hematopoietic stem cells	blood
40	chr19:56651200-56651400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr19:56651200-56651400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:56651200-56651400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr19:56651200-56651400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:56651200-56651400	Enhancers	Adipose Nuclei	Adipose
45	chr19:56651200-56651400	Enhancers	Aorta	Aorta
46	chr19:56651200-56651400	Enhancers	Brain Angular Gyrus	brain
47	chr19:56651200-56651400	Enhancers	Brain Anterior Caudate	brain
48	chr19:56651200-56651400	Enhancers	Brain Cingulate Gyrus	brain
49	chr19:56651200-56651400	Enhancers	Brain Germinal Matrix	brain
50	chr19:56651200-56651400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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