Variant report

Variant	rs12610409
Chromosome Location	chr19:39394271-39394272
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39388731..39393423-chr19:39394024..39400037,10	K562	blood:
2	chr19:39337724..39340689-chr19:39393839..39396661,3	K562	blood:
3	chr19:39391259..39393276-chr19:39393440..39395044,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104825	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10410544	0.86[ASN][1000 genomes]
rs10416055	0.85[ASN][1000 genomes]
rs10775533	0.92[ASN][1000 genomes]
rs11083485	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11083489	0.92[ASN][1000 genomes]
rs11668245	0.92[ASN][1000 genomes]
rs12462710	0.92[ASN][1000 genomes]
rs12972925	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12972986	0.92[ASN][1000 genomes]
rs12979755	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17545254	0.92[ASN][1000 genomes]
rs1808662	0.92[ASN][1000 genomes]
rs1865047	0.85[ASN][1000 genomes]
rs3136640	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801971	0.92[ASN][1000 genomes]
rs4802998	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803006	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803034	0.92[ASN][1000 genomes]
rs575	0.92[ASN][1000 genomes]
rs7257007	0.92[ASN][1000 genomes]
rs730078	0.85[ASN][1000 genomes]
rs7508411	0.92[ASN][1000 genomes]
rs7508539	0.92[ASN][1000 genomes]
rs9636109	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749516	0.92[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	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
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv911674	chr19:39391547-39398631	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv911675	chr19:39394271-39398631	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391000-39394800	Weak transcription	Spleen	Spleen
2	chr19:39391000-39395000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:39391000-39395800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:39391200-39394800	Weak transcription	Gastric	stomach
5	chr19:39391200-39395000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr19:39391200-39395200	Weak transcription	Pancreas	Pancrea
7	chr19:39391200-39395400	Weak transcription	Aorta	Aorta
8	chr19:39391200-39395400	Weak transcription	Esophagus	oesophagus
9	chr19:39391200-39395600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
11	chr19:39391400-39395200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:39391400-39395600	Weak transcription	Brain Germinal Matrix	brain
13	chr19:39391400-39397400	Weak transcription	Fetal Brain Female	brain
14	chr19:39391400-39397600	Weak transcription	Psoas Muscle	Psoas
15	chr19:39391400-39402200	Weak transcription	Fetal Brain Male	brain
16	chr19:39391600-39394800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:39391600-39395000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr19:39391600-39395000	Weak transcription	NHDF-Ad	bronchial
19	chr19:39391600-39395200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr19:39391600-39395200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:39391600-39395200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:39391600-39395200	Weak transcription	Colonic Mucosa	Colon
23	chr19:39391600-39395200	Weak transcription	Ovary	ovary
24	chr19:39391600-39395200	Weak transcription	Right Ventricle	heart
25	chr19:39391600-39397800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:39391600-39414800	Weak transcription	HMEC	breast
27	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
28	chr19:39391800-39394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:39391800-39395000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:39391800-39395000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:39391800-39395000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr19:39391800-39395000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:39391800-39395000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:39391800-39395000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:39391800-39395000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:39391800-39395000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr19:39391800-39395000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:39391800-39395000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:39391800-39395200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:39391800-39395200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:39391800-39395200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:39391800-39395200	Weak transcription	Brain Substantia Nigra	brain
43	chr19:39391800-39395200	Weak transcription	Colon Smooth Muscle	Colon
44	chr19:39391800-39395200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:39391800-39395200	Weak transcription	Thymus	Thymus
46	chr19:39391800-39395400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:39391800-39395400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:39391800-39395400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr19:39391800-39395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:39391800-39395600	Weak transcription	NHLF	lung

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