Variant report

Variant	rs1654623
Chromosome Location	chr19:42869556-42869557
allele	A/C
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	SP1	chr19:42869358-42869695	GM12878	blood:	n/a	chr19:42869496-42869510 chr19:42869470-42869480 chr19:42869470-42869480
2	EP300	chr19:42869461-42869700	GM12878	blood:	n/a	n/a
3	TBP	chr19:42869508-42869700	GM12878	blood:	n/a	n/a
4	EBF1	chr19:42869195-42869735	GM12878	blood:	n/a	chr19:42869534-42869544 chr19:42869533-42869544
5	BHLHE40	chr19:42869443-42869688	GM12878	blood:	n/a	n/a
6	CUX1	chr19:42869314-42869721	GM12878	blood:	n/a	n/a
7	EBF1	chr19:42868898-42869789	GM12878	blood:	n/a	chr19:42869534-42869544 chr19:42869533-42869544
8	RCOR1	chr19:42869385-42869655	GM12878	blood:	n/a	n/a
9	EBF1	chr19:42869143-42869771	GM12878	blood:	n/a	chr19:42869534-42869544 chr19:42869533-42869544
10	ZNF143	chr19:42869530-42869574	GM12878	blood:	n/a	n/a
11	MXI1	chr19:42869367-42869567	GM12878	blood:	n/a	n/a
12	STAT3	chr19:42869435-42869698	GM12878	blood:	n/a	chr19:42869526-42869538
13	PAX5	chr19:42869339-42869637	GM12878	blood:	n/a	n/a
14	CTCF	chr19:42869480-42869630	HRE	kidney:	n/a	n/a
15	MAZ	chr19:42869234-42869659	GM12878	blood:	n/a	chr19:42869406-42869416
16	MAX	chr19:42869371-42869565	GM12878	blood:	n/a	chr19:42869406-42869416
17	RUNX3	chr19:42869073-42869774	GM12878	blood:	n/a	chr19:42869248-42869263

No.	Distal block	Cell Line	Cell type
1	chr19:42865401..42867644-chr19:42869322..42871775,2	MCF-7	breast:
2	chr19:42858212..42860200-chr19:42868262..42870345,2	K562	blood:
3	chr19:42862702..42865625-chr19:42867333..42870442,3	K562	blood:

Variant related genes	Relation type
MEGF8	TF binding region
ENSG00000105429	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10410185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs10410198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs10410698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs10412833	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11878620	0.82[CHB][hapmap]
rs11880124	0.82[CHB][hapmap]
rs11883412	0.82[CHB][hapmap]
rs1206009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1206027	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1206028	1.00[ASW][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1206029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1206031	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1206033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1206035	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1206038	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1206040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1206041	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1206042	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1206043	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1206044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209280	0.87[EUR][1000 genomes]
rs1211265	0.87[EUR][1000 genomes]
rs13346991	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1613100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676211	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1676213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676214	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1676220	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1676221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1676222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1685565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16975684	0.82[CHB][hapmap]
rs2267630	1.00[CHB][hapmap]
rs2302485	0.82[CHB][hapmap]
rs2303652	0.82[CHB][hapmap]
rs2537697	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs2615614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.91[EUR][1000 genomes]
rs28537976	0.82[EUR][1000 genomes]
rs28621009	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34922891	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35557987	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745231	0.82[CHB][hapmap]
rs3745233	0.82[CHB][hapmap]
rs3810148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs3810151	0.82[CHB][hapmap]
rs4141062	1.00[CHB][hapmap]
rs61995685	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7248379	0.82[CHB][hapmap]
rs7255956	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7260287	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73552881	0.82[EUR][1000 genomes]
rs73552895	0.91[EUR][1000 genomes]
rs741070	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs8182491	0.82[CHB][hapmap]
rs851292	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs851293	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs851294	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851615	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs862228	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs865436	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9636121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription 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	70 gene(s)	inside rSNPs	diseases
6	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42830800-42879200	Weak transcription	Small Intestine	intestine
2	chr19:42830800-42884200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr19:42831000-42874400	Weak transcription	HSMM	muscle
4	chr19:42831600-42882600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr19:42831800-42873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:42831800-42874800	Weak transcription	K562	blood
7	chr19:42844800-42877400	Weak transcription	Stomach Mucosa	stomach
8	chr19:42857400-42869600	Strong transcription	Brain Germinal Matrix	brain
9	chr19:42857600-42870800	Strong transcription	Fetal Brain Female	brain
10	chr19:42857800-42871000	Weak transcription	Fetal Brain Male	brain
11	chr19:42857800-42874000	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:42858200-42872200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:42862400-42873800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:42862600-42878800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:42863600-42874800	Weak transcription	HUVEC	blood vessel
16	chr19:42865200-42869600	Strong transcription	Pancreas	Pancrea
17	chr19:42865200-42873800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:42866600-42871600	Enhancers	Primary B cells from peripheral blood	blood
19	chr19:42866800-42869800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:42867200-42871000	Enhancers	Primary B cells from cord blood	blood
21	chr19:42867800-42869600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:42868400-42869800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:42868400-42870200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr19:42868400-42870600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:42868400-42870600	Weak transcription	HSMMtube	muscle
26	chr19:42868400-42871600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:42868400-42873800	Weak transcription	Placenta	Placenta
28	chr19:42868400-42874000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:42868400-42874400	Strong transcription	Fetal Intestine Small	intestine
30	chr19:42868400-42874800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr19:42868400-42874800	Weak transcription	NHLF	lung
32	chr19:42868400-42874800	Weak transcription	Osteobl	bone
33	chr19:42868400-42876200	Weak transcription	Lung	lung
34	chr19:42868400-42879200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:42868400-42881400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:42868400-42882400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:42868600-42869800	Enhancers	Adipose Nuclei	Adipose
38	chr19:42868600-42869800	Genic enhancers	Fetal Muscle Leg	muscle
39	chr19:42868600-42870600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:42868600-42873600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr19:42868600-42873800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:42868600-42873800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr19:42868600-42874000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr19:42868600-42878800	Weak transcription	Esophagus	oesophagus
45	chr19:42868600-42878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr19:42868600-42879000	Weak transcription	Aorta	Aorta
47	chr19:42868600-42882600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr19:42868800-42869800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:42868800-42869800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr19:42868800-42870600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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