Variant report

Variant	rs1206041
Chromosome Location	chr19:42861293-42861294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42854805..42859477-chr19:42860532..42863518,6	K562	blood:
2	chr19:42855415..42858223-chr19:42859630..42862588,2	MCF-7	breast:
3	chr19:42859791..42861362-chr19:42867792..42869534,2	K562	blood:

Variant related genes	Relation type
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];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10410198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10410698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10412833	0.85[AMR][1000 genomes];0.91[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];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.93[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];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]
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];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[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];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1206031	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[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];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1206035	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1206040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1206042	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1206043	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1206044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209280	0.89[EUR][1000 genomes]
rs1211265	0.89[EUR][1000 genomes]
rs13346991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];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]
rs1654623	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]
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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676213	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1676214	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1676215	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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];1.00[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1676220	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1676221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1676222	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1685565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][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];0.88[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2615614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28537976	0.84[EUR][1000 genomes]
rs28621009	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34922891	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35557987	0.95[EUR][1000 genomes];1.00[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];0.94[TSI][hapmap]
rs3810151	0.82[CHB][hapmap]
rs4141062	1.00[CHB][hapmap]
rs61995685	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248379	0.82[CHB][hapmap]
rs7255956	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7260287	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73552881	0.84[EUR][1000 genomes]
rs73552895	0.93[EUR][1000 genomes]
rs741070	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs8182491	0.82[CHB][hapmap]
rs851292	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851293	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851294	0.86[EUR][1000 genomes];0.92[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];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs851615	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs862228	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs865436	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9636121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42830800-42867200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:42830800-42867600	Weak transcription	Fetal Kidney	kidney
3	chr19:42830800-42879200	Weak transcription	Small Intestine	intestine
4	chr19:42830800-42884200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:42831000-42874400	Weak transcription	HSMM	muscle
6	chr19:42831400-42867400	Weak transcription	Fetal Heart	heart
7	chr19:42831400-42867400	Weak transcription	NHEK	skin
8	chr19:42831600-42861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:42831600-42882600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr19:42831800-42873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:42831800-42874800	Weak transcription	K562	blood
12	chr19:42833400-42867400	Weak transcription	GM12878-XiMat	blood
13	chr19:42835400-42867400	Strong transcription	Fetal Stomach	stomach
14	chr19:42839800-42866800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:42841000-42867600	Weak transcription	Osteobl	bone
16	chr19:42841400-42865000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr19:42841600-42867800	Weak transcription	HepG2	liver
18	chr19:42843400-42867800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:42844000-42861800	Strong transcription	Fetal Intestine Small	intestine
20	chr19:42844000-42867200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr19:42844800-42877400	Weak transcription	Stomach Mucosa	stomach
22	chr19:42849800-42867400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:42851000-42863600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr19:42851600-42862000	Strong transcription	Fetal Intestine Large	intestine
25	chr19:42852000-42862800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:42852000-42863600	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:42852000-42864000	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:42852000-42868000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:42852000-42868600	Strong transcription	Fetal Muscle Leg	muscle
30	chr19:42852200-42863200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:42852200-42864000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:42852200-42867400	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:42852200-42867800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:42852200-42867800	Strong transcription	Right Ventricle	heart
35	chr19:42852400-42867200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr19:42852400-42867800	Weak transcription	Primary T cells from cord blood	blood
37	chr19:42853000-42867400	Strong transcription	Lung	lung
38	chr19:42853600-42862800	Strong transcription	Esophagus	oesophagus
39	chr19:42853800-42863200	Strong transcription	Brain Hippocampus Middle	brain
40	chr19:42854200-42867400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:42854600-42862600	Strong transcription	Ovary	ovary
42	chr19:42855000-42867400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr19:42855200-42862600	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr19:42855200-42863600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:42855400-42861400	Strong transcription	Pancreas	Pancrea
46	chr19:42855400-42862400	Strong transcription	Colonic Mucosa	Colon
47	chr19:42855400-42863600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:42855400-42868000	Strong transcription	Left Ventricle	heart
49	chr19:42855600-42863000	Strong transcription	Adipose Nuclei	Adipose
50	chr19:42855600-42863000	Strong transcription	Gastric	stomach

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