Variant report

Variant	rs10421861
Chromosome Location	chr19:44351107-44351108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44325529..44327372-chr19:44349912..44351479,2	K562	blood:
2	chr19:44346181..44347972-chr19:44350637..44353162,2	K562	blood:
3	chr19:44342723..44344793-chr19:44350333..44352152,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRGC-4	chr19:44351092-44351486	NONHSAT066634

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1036246	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10405318	0.84[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10408461	0.86[GIH][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs10412955	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10415344	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10416116	0.84[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10500286	0.86[GIH][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs10500287	0.90[EUR][1000 genomes]
rs11878787	0.81[EUR][1000 genomes]
rs11879541	0.93[EUR][1000 genomes]
rs11880651	0.94[EUR][1000 genomes]
rs12608578	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs13344589	0.99[EUR][1000 genomes]
rs1549953	0.88[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1549954	0.84[CEU][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1549955	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1549956	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1549957	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1549959	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1565057	0.89[EUR][1000 genomes]
rs17712224	0.94[EUR][1000 genomes]
rs1909	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1964381	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1994414	0.84[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1994415	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1994416	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2016345	0.89[EUR][1000 genomes]
rs2163855	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2195981	0.83[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2217669	0.83[CEU][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2356401	0.86[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2356403	0.81[EUR][1000 genomes]
rs2356432	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2356433	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2356434	0.84[CEU][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2356438	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2356439	0.84[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs239948	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs239949	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2883946	0.84[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap]
rs349032	0.84[GIH][hapmap]
rs4511643	0.84[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs57096959	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs57133938	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs59503823	0.81[EUR][1000 genomes]
rs60036744	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs60085895	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs62114569	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs62118368	0.99[EUR][1000 genomes]
rs62118369	0.99[EUR][1000 genomes]
rs62118371	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs62118372	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6509120	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7247308	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7247863	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7248807	0.83[EUR][1000 genomes]
rs7249057	0.81[EUR][1000 genomes]
rs7249413	0.83[CEU][hapmap]
rs7253002	0.84[CEU][hapmap];0.99[EUR][1000 genomes]
rs7253384	0.84[CEU][hapmap];0.99[EUR][1000 genomes]
rs7253606	0.84[CEU][hapmap];0.99[EUR][1000 genomes]
rs7254659	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7259647	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs73052639	0.94[EUR][1000 genomes]
rs73052665	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs8099861	0.83[CEU][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs8106802	0.88[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs8112065	0.84[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs8113286	0.84[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv458710	chr19:44339960-44410846	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv579853	chr19:44339960-44410846	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44332800-44357200	ZNF genes & repeats	Liver	Liver
2	chr19:44333600-44357400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:44334000-44353200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:44335200-44357200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:44335200-44368200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:44335400-44357200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:44335400-44366600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr19:44336600-44357600	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr19:44336800-44353000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr19:44336800-44356800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr19:44336800-44357200	ZNF genes & repeats	Fetal Lung	lung
12	chr19:44338000-44352800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:44339000-44352800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
14	chr19:44339000-44355400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
15	chr19:44339200-44355400	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr19:44339200-44355400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
17	chr19:44339200-44357200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:44339400-44352600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr19:44339400-44352600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:44339400-44355400	ZNF genes & repeats	Primary T cells from cord blood	blood
21	chr19:44339400-44355600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:44339600-44355400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
23	chr19:44340800-44353000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:44341000-44352600	ZNF genes & repeats	Fetal Intestine Large	intestine
25	chr19:44341000-44354200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
26	chr19:44341000-44355400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr19:44341000-44357200	ZNF genes & repeats	Brain Anterior Caudate	brain
28	chr19:44341200-44354800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr19:44341200-44357200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:44342000-44353000	ZNF genes & repeats	NH-A	brain
31	chr19:44342200-44355400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
32	chr19:44343000-44352800	ZNF genes & repeats	Fetal Kidney	kidney
33	chr19:44345800-44355400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
34	chr19:44347000-44351400	Weak transcription	Stomach Mucosa	stomach
35	chr19:44347000-44351800	Weak transcription	Fetal Thymus	thymus
36	chr19:44347600-44354600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:44347600-44354600	Weak transcription	Fetal Stomach	stomach
38	chr19:44348600-44355400	ZNF genes & repeats	HSMM	muscle
39	chr19:44348600-44357000	ZNF genes & repeats	Fetal Brain Female	brain
40	chr19:44349200-44351400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:44349200-44357200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:44349800-44352600	ZNF genes & repeats	Colonic Mucosa	Colon
43	chr19:44349800-44353000	ZNF genes & repeats	K562	blood
44	chr19:44349800-44354600	ZNF genes & repeats	Fetal Heart	heart
45	chr19:44349800-44355200	ZNF genes & repeats	NHEK	skin
46	chr19:44350000-44354000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
47	chr19:44350400-44352400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:44350400-44352600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:44350400-44352600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
50	chr19:44350400-44352600	ZNF genes & repeats	Fetal Brain Male	brain

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