Variant report

Variant	rs677142
Chromosome Location	chr19:56610377-56610378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56606614..56610711-chr19:56622862..56625649,3	MCF-7	breast:
2	chr19:56609509..56612797-chr19:56648982..56652625,3	K562	blood:
3	chr19:56589626..56592403-chr19:56608296..56610728,2	MCF-7	breast:
4	chr19:56609156..56614023-chr19:56614843..56617057,5	K562	blood:
5	chr19:56606956..56610411-chr19:56610787..56614898,5	K562	blood:

Variant related genes	Relation type
ENSG00000142409	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000223060	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1007851	0.85[ASN][1000 genomes]
rs12459102	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2450439	0.81[ASN][1000 genomes]
rs2631627	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2631628	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2631631	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2631637	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631640	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2637092	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2637094	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2637097	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2932757	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35766803	0.85[ASN][1000 genomes]
rs473953	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs478402	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs481936	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490345	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs492078	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497453	0.82[AMR][1000 genomes]
rs501798	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504350	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs506547	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs506782	0.94[EUR][1000 genomes]
rs509897	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs517021	0.84[AMR][1000 genomes]
rs517582	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521092	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs522980	0.80[AMR][1000 genomes]
rs524778	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs524829	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs524988	0.82[ASN][1000 genomes]
rs525827	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs526275	0.87[EUR][1000 genomes]
rs527715	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs530102	1.00[EUR][1000 genomes]
rs533640	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533734	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535393	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs536342	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536414	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537425	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs540900	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs547945	0.82[AMR][1000 genomes]
rs554681	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs564050	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570210	0.93[ASN][1000 genomes]
rs572851	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs578990	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs578991	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs582271	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583330	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs588574	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592827	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs599405	0.85[AMR][1000 genomes]
rs604364	0.85[ASN][1000 genomes]
rs609736	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609755	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs619934	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626821	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs629544	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs630704	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs640654	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs642776	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs643133	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs643174	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs648352	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6509982	0.85[ASN][1000 genomes]
rs659424	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs662308	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs662763	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs665082	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs665846	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs665857	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs667438	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs667974	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs668056	1.00[EUR][1000 genomes]
rs677127	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs678540	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs684653	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs685117	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250351	0.85[ASN][1000 genomes]

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	esv3352645	chr19:56609090-56611088	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56592600-56620000	Weak transcription	HSMMtube	muscle
2	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:56593000-56616200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:56593000-56616600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:56593000-56616800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:56593600-56616000	Weak transcription	Stomach Mucosa	stomach
8	chr19:56594800-56616800	Weak transcription	HUVEC	blood vessel
9	chr19:56596600-56614800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:56597200-56619400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:56599800-56615200	Strong transcription	Liver	Liver
12	chr19:56600000-56619000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:56600400-56614400	Strong transcription	HepG2	liver
14	chr19:56600800-56616800	Weak transcription	Small Intestine	intestine
15	chr19:56601400-56612000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:56601600-56611800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:56602800-56614400	ZNF genes & repeats	Fetal Stomach	stomach
18	chr19:56602800-56620000	Weak transcription	NH-A	brain
19	chr19:56603000-56616600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:56603200-56612400	Weak transcription	Osteobl	bone
21	chr19:56603200-56619800	Weak transcription	NHDF-Ad	bronchial
22	chr19:56603800-56612200	Weak transcription	Brain Substantia Nigra	brain
23	chr19:56603800-56616800	Weak transcription	Psoas Muscle	Psoas
24	chr19:56604000-56614800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr19:56604200-56611600	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:56604800-56616200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:56604800-56616800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:56605000-56612200	Weak transcription	Aorta	Aorta
29	chr19:56605000-56612600	Weak transcription	HMEC	breast
30	chr19:56605000-56614400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr19:56605000-56615000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:56605000-56616400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:56605200-56610800	Weak transcription	Primary B cells from cord blood	blood
34	chr19:56605200-56615000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:56605200-56615000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:56605200-56617000	Weak transcription	Brain Angular Gyrus	brain
37	chr19:56605200-56619800	Weak transcription	HSMM	muscle
38	chr19:56605200-56620000	Weak transcription	Fetal Kidney	kidney
39	chr19:56605400-56610400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:56605400-56612600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:56605400-56615000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:56605600-56615000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr19:56605600-56615000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:56606000-56615800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:56606200-56611200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:56606200-56612400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:56606200-56614200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr19:56606200-56615000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:56606200-56615200	Strong transcription	Colonic Mucosa	Colon
50	chr19:56606200-56615200	Strong transcription	Thymus	Thymus

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