Variant report

Variant	rs62121816
Chromosome Location	chr19:39164464-39164465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39148867..39151861-chr19:39164065..39166508,2	K562	blood:
2	chr19:39154116..39156228-chr19:39162782..39165101,2	K562	blood:
3	chr19:39138117..39140492-chr19:39163770..39166162,3	K562	blood:
4	chr19:39163941..39166485-chr19:39290106..39293059,2	K562	blood:
5	chr19:39164276..39166665-chr19:39166865..39169150,2	K562	blood:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10403540	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10404257	0.82[ASN][1000 genomes]
rs10406778	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10415219	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10415646	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10421560	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11083475	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12460849	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12462270	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13343794	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16972767	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279144	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2303040	0.81[EUR][1000 genomes]
rs28488032	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28624276	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3745859	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3786835	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3786837	0.88[EUR][1000 genomes]
rs3786839	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3786845	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3786848	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3786851	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3810341	0.89[ASN][1000 genomes]
rs55876653	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56113315	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56365761	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62121814	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62121818	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7251903	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7252589	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254100	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111746	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883394	0.91[EUR][1000 genomes]
rs883433	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs979971	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs979972	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 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	chr19:39156600-39164800	Enhancers	Fetal Heart	heart
2	chr19:39158800-39167600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:39159000-39165000	Weak transcription	Hela-S3	cervix
4	chr19:39159000-39166600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:39159000-39166800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:39159600-39169600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:39160400-39173400	Weak transcription	Brain Germinal Matrix	brain
8	chr19:39160600-39165200	Weak transcription	Dnd41	blood
9	chr19:39161000-39164600	Weak transcription	GM12878-XiMat	blood
10	chr19:39161000-39164800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:39161000-39166800	Weak transcription	Primary T cells from cord blood	blood
12	chr19:39161200-39164600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr19:39161200-39164800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:39161200-39164800	Weak transcription	Esophagus	oesophagus
15	chr19:39161200-39164800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr19:39161200-39165000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:39161200-39166000	Weak transcription	Primary B cells from cord blood	blood
18	chr19:39161200-39176000	Weak transcription	Fetal Brain Male	brain
19	chr19:39161200-39176000	Weak transcription	Fetal Brain Female	brain
20	chr19:39161600-39164600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr19:39161600-39164800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:39161800-39164800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr19:39161800-39164800	Weak transcription	NHLF	lung
24	chr19:39161800-39165200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:39162000-39164800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr19:39162000-39165000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr19:39162000-39165400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:39162200-39164800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr19:39162200-39164800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:39162200-39165400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr19:39162200-39173400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:39162400-39165200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:39162400-39165400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr19:39162400-39172000	Enhancers	Left Ventricle	heart
35	chr19:39162600-39164600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:39162600-39164600	Weak transcription	HMEC	breast
37	chr19:39162600-39164800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:39162600-39164800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:39162600-39164800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr19:39162600-39164800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:39162600-39164800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr19:39162600-39164800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:39162600-39164800	Weak transcription	Fetal Kidney	kidney
44	chr19:39162600-39165000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:39162600-39169400	Genic enhancers	A549	lung
46	chr19:39162800-39164600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr19:39162800-39164600	Weak transcription	Brain Substantia Nigra	brain
48	chr19:39162800-39164600	Weak transcription	Fetal Lung	lung
49	chr19:39162800-39164600	Weak transcription	Fetal Stomach	stomach
50	chr19:39162800-39164600	Weak transcription	Stomach Mucosa	stomach

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