Variant report

Variant	rs10854009
Chromosome Location	chr19:19284705-19284706
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19249614..19251216-chr19:19284548..19287281,2	K562	blood:
2	chr19:19248991..19251114-chr19:19283513..19286048,2	K562	blood:
3	chr19:19255404..19257659-chr19:19284521..19286455,2	MCF-7	breast:
4	chr19:19280728..19282635-chr19:19282932..19284742,2	K562	blood:
5	chr19:19284622..19286518-chr19:19409088..19411298,2	K562	blood:
6	chr19:19284383..19288612-chr19:19288854..19291941,5	MCF-7	breast:
7	chr19:19279646..19282123-chr19:19284423..19286366,3	K562	blood:

Variant related genes	Relation type
ENSG00000254901	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064545	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10417796	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10418053	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050544	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854008	0.83[EUR][1000 genomes]
rs10854012	0.83[EUR][1000 genomes]
rs11085253	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11669408	0.82[EUR][1000 genomes]
rs11669860	0.87[AMR][1000 genomes]
rs12609573	0.83[EUR][1000 genomes]
rs12972894	0.81[EUR][1000 genomes]
rs12974672	0.83[EUR][1000 genomes]
rs12975096	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12975253	0.83[EUR][1000 genomes]
rs12975290	0.83[EUR][1000 genomes]
rs12980955	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12981160	0.81[EUR][1000 genomes]
rs1858846	0.83[EUR][1000 genomes]
rs2238668	0.83[EUR][1000 genomes]
rs2239369	0.85[EUR][1000 genomes]
rs2239370	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283623	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2314035	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35342977	0.83[EUR][1000 genomes]
rs3787040	0.81[EUR][1000 genomes]
rs4808185	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs539	0.84[EUR][1000 genomes]
rs62135499	0.82[EUR][1000 genomes]
rs71332145	0.82[EUR][1000 genomes]
rs7250650	0.84[EUR][1000 genomes]
rs7256802	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7256811	0.83[EUR][1000 genomes]
rs7260127	0.82[EUR][1000 genomes]
rs72997174	0.82[EUR][1000 genomes]
rs741706	0.83[EUR][1000 genomes]
rs759999	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8101388	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19259000-19290200	Weak transcription	Colon Smooth Muscle	Colon
2	chr19:19268800-19287200	Weak transcription	Dnd41	blood
3	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
4	chr19:19280800-19287000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:19280800-19301600	Weak transcription	NHEK	skin
6	chr19:19281000-19287000	Weak transcription	Primary T cells from cord blood	blood
7	chr19:19281200-19287400	Weak transcription	Aorta	Aorta
8	chr19:19281400-19285600	Weak transcription	Right Ventricle	heart
9	chr19:19281400-19286600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:19281400-19287000	Weak transcription	Gastric	stomach
11	chr19:19281400-19287000	Weak transcription	Lung	lung
12	chr19:19281400-19287000	Weak transcription	Thymus	Thymus
13	chr19:19281400-19287400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr19:19281400-19287400	Weak transcription	Esophagus	oesophagus
15	chr19:19281400-19287400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:19281400-19290200	Weak transcription	Brain Substantia Nigra	brain
17	chr19:19281400-19292200	Weak transcription	HMEC	breast
18	chr19:19281400-19300800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr19:19281600-19285800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:19281600-19286400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:19281600-19286600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:19281600-19287200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr19:19281600-19287200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:19281600-19287200	Weak transcription	Fetal Intestine Large	intestine
25	chr19:19281600-19287400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:19281600-19289000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:19281600-19290400	Weak transcription	Fetal Lung	lung
28	chr19:19281600-19290600	Weak transcription	Fetal Brain Female	brain
29	chr19:19281600-19290800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr19:19281600-19290800	Weak transcription	Brain Angular Gyrus	brain
31	chr19:19281600-19292000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:19281600-19293000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr19:19281600-19297200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr19:19281600-19299400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr19:19281600-19300600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:19281600-19302000	Weak transcription	NH-A	brain
37	chr19:19281600-19302200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:19281800-19285800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:19281800-19285800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:19281800-19286400	Weak transcription	Fetal Intestine Small	intestine
41	chr19:19281800-19286600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:19281800-19286600	Weak transcription	Fetal Thymus	thymus
43	chr19:19281800-19286600	Weak transcription	Ovary	ovary
44	chr19:19281800-19286800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:19281800-19287000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:19281800-19287000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr19:19281800-19287000	Weak transcription	Pancreas	Pancrea
48	chr19:19281800-19287400	Weak transcription	Brain Anterior Caudate	brain
49	chr19:19281800-19287400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:19281800-19287400	Weak transcription	Colonic Mucosa	Colon

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