Variant report

Variant	rs12979229
Chromosome Location	chr19:55909768-55909769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:55686466..55688943-chr19:55909341..55911535,2	K562	blood:
2	chr19:55737915..55740196-chr19:55909661..55911282,2	K562	blood:
3	chr19:55908700..55911524-chr19:56015607..56017274,2	K562	blood:
4	chr19:55909744..55913358-chr19:55997717..56001739,3	K562	blood:
5	chr19:55907236..55909788-chr19:55985827..55987886,2	K562	blood:
6	chr19:55908160..55910200-chr19:56015121..56017107,2	K562	blood:
7	chr19:55684707..55688022-chr19:55908129..55911789,4	K562	blood:

Variant related genes	Relation type
ENSG00000129990	Chromatin interaction
ENSG00000179954	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000269808	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000180089	Chromatin interaction
ENSG00000269859	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10403361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414353	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10415761	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1124917	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12460492	0.86[ASN][1000 genomes]
rs12462594	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12977195	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12977341	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12985701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13343706	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16986359	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28411209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454071	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28635028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891577	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73606242	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73619625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
2	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
4	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
5	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
6	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
7	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer 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 miRNA target site	203 gene(s)	inside rSNPs	diseases
8	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
9	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
10	nsv544085	chr19:55875808-55911275	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 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	chr19:55899200-55913400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:55900200-55918400	Weak transcription	Psoas Muscle	Psoas
3	chr19:55900400-55911800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr19:55900600-55917600	Weak transcription	Stomach Mucosa	stomach
5	chr19:55901000-55917800	Weak transcription	Right Atrium	heart
6	chr19:55901200-55913200	Weak transcription	Small Intestine	intestine
7	chr19:55901400-55912000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:55901600-55911800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:55901600-55911800	Weak transcription	HUVEC	blood vessel
10	chr19:55901600-55912000	Weak transcription	HSMM	muscle
11	chr19:55901600-55914400	Weak transcription	Fetal Kidney	kidney
12	chr19:55901800-55911800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:55901800-55911800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:55901800-55916800	Weak transcription	Fetal Brain Male	brain
15	chr19:55902000-55911800	Weak transcription	Ovary	ovary
16	chr19:55902000-55912200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr19:55902200-55910800	Weak transcription	Esophagus	oesophagus
18	chr19:55902200-55911600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:55902200-55911800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr19:55902200-55912400	Weak transcription	Colonic Mucosa	Colon
21	chr19:55902200-55917400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:55902400-55911600	Weak transcription	NH-A	brain
23	chr19:55902400-55912000	Weak transcription	Aorta	Aorta
24	chr19:55902600-55911600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:55902600-55911800	Weak transcription	HMEC	breast
26	chr19:55902800-55911000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:55903000-55910800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:55903000-55910800	Weak transcription	Fetal Muscle Leg	muscle
29	chr19:55903000-55911200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:55903000-55911400	Weak transcription	Brain Germinal Matrix	brain
31	chr19:55903000-55911800	Weak transcription	Brain Substantia Nigra	brain
32	chr19:55903000-55911800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr19:55903000-55911800	Weak transcription	NHDF-Ad	bronchial
34	chr19:55903000-55912000	Weak transcription	Brain Angular Gyrus	brain
35	chr19:55903000-55912000	Weak transcription	Gastric	stomach
36	chr19:55903000-55912000	Weak transcription	Pancreas	Pancrea
37	chr19:55903000-55913200	Weak transcription	Fetal Lung	lung
38	chr19:55903000-55914000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr19:55903200-55909800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:55903200-55911200	Weak transcription	Brain Hippocampus Middle	brain
41	chr19:55903200-55911600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:55903200-55911800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:55903200-55911800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:55903200-55911800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:55903400-55911200	Weak transcription	Fetal Thymus	thymus
46	chr19:55903400-55911600	Weak transcription	Hela-S3	cervix
47	chr19:55903400-55911800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:55903400-55911800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:55903400-55911800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr19:55903400-55911800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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