Variant report

Variant	rs41275796
Chromosome Location	chr19:52693540-52693541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52641405..52644253-chr19:52691691..52696539,6	MCF-7	breast:
2	chr19:52692900..52696088-chr19:52702014..52707428,7	MCF-7	breast:
3	chr19:52598726..52600984-chr19:52691577..52693709,2	MCF-7	breast:
4	chr19:52597423..52599077-chr19:52692134..52694986,2	K562	blood:
5	chr1:17221697..17224418-chr19:52692331..52695072,2	MCF-7	breast:
6	chr19:52638083..52640348-chr19:52693399..52695139,2	MCF-7	breast:
7	chr19:52641479..52644491-chr19:52690575..52695402,7	MCF-7	breast:
8	chr19:52641692..52643573-chr19:52692556..52694474,2	K562	blood:
9	chr19:52692960..52694798-chr19:52714697..52716755,2	K562	blood:
10	chr19:52671404..52675593-chr19:52690586..52694996,6	MCF-7	breast:
11	chr19:52693323..52694045-chr5:10760778..10761529,2	Hela-S3	cervix:
12	chr19:52691967..52694543-chr19:52715939..52718199,3	MCF-7	breast:
13	chr19:52642060..52644482-chr19:52693480..52696819,3	K562	blood:
14	chr19:52691998..52694919-chr19:53605403..53608321,3	K562	blood:
15	chr19:52692325..52695090-chr19:52733176..52735417,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000112977	Chromatin interaction
ENSG00000105568	Chromatin interaction
ENSG00000204611	Chromatin interaction
ENSG00000268015	Chromatin interaction
ENSG00000196267	Chromatin interaction
ENSG00000267927	Chromatin interaction
ENSG00000207005	Chromatin interaction
ENSG00000272324	Chromatin interaction
ENSG00000197608	Chromatin interaction
ENSG00000170949	Chromatin interaction
ENSG00000256087	Chromatin interaction
ENSG00000267827	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10409071	1.00[ASN][1000 genomes]
rs10416397	1.00[ASN][1000 genomes]
rs11537695	1.00[ASN][1000 genomes]
rs13382052	1.00[ASN][1000 genomes]
rs41275802	1.00[ASN][1000 genomes]
rs56071533	1.00[ASN][1000 genomes]
rs58576324	1.00[ASN][1000 genomes]
rs61285115	1.00[ASN][1000 genomes]
rs717322	1.00[ASN][1000 genomes]
rs73934406	1.00[ASN][1000 genomes]
rs73934407	1.00[ASN][1000 genomes]
rs73935029	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935031	1.00[ASN][1000 genomes]
rs73935032	1.00[ASN][1000 genomes]
rs73935039	1.00[ASN][1000 genomes]
rs73935040	1.00[ASN][1000 genomes]
rs73935041	1.00[ASN][1000 genomes]
rs73935044	1.00[ASN][1000 genomes]
rs73935048	1.00[ASN][1000 genomes]
rs73935050	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv21017	chr19:52692555-52696215	Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52691600-52694600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:52691800-52694400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:52691800-52694600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:52691800-52694600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:52692000-52694200	Active TSS	Right Atrium	heart
6	chr19:52692000-52694400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:52692000-52694400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:52692000-52694400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:52692000-52694400	Active TSS	Psoas Muscle	Psoas
10	chr19:52692000-52694600	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr19:52692000-52694600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr19:52692000-52694800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:52692000-52694800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:52692000-52695400	Active TSS	Left Ventricle	heart
15	chr19:52692200-52693800	Active TSS	HepG2	liver
16	chr19:52692200-52694200	Active TSS	Gastric	stomach
17	chr19:52692200-52694400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr19:52692200-52694400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:52692200-52694400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:52692200-52694400	Active TSS	Aorta	Aorta
21	chr19:52692200-52694400	Active TSS	Esophagus	oesophagus
22	chr19:52692200-52694600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr19:52692200-52694600	Active TSS	GM12878-XiMat	blood
24	chr19:52692200-52694800	Active TSS	Lung	lung
25	chr19:52692200-52694800	Active TSS	Ovary	ovary
26	chr19:52692400-52693600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:52692400-52694000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:52692400-52694000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:52692400-52694000	Active TSS	Thymus	Thymus
30	chr19:52692400-52694200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:52692400-52694200	Active TSS	Liver	Liver
32	chr19:52692400-52694200	Active TSS	Brain Angular Gyrus	brain
33	chr19:52692400-52694200	Active TSS	Brain Cingulate Gyrus	brain
34	chr19:52692400-52694200	Active TSS	Brain Germinal Matrix	brain
35	chr19:52692400-52694200	Active TSS	Brain Substantia Nigra	brain
36	chr19:52692400-52694200	Active TSS	Colonic Mucosa	Colon
37	chr19:52692400-52694200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:52692400-52694200	Active TSS	Fetal Brain Male	brain
39	chr19:52692400-52694200	Active TSS	Pancreas	Pancrea
40	chr19:52692400-52694200	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr19:52692400-52694200	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr19:52692400-52694200	Active TSS	Rectal Smooth Muscle	rectum
43	chr19:52692400-52694400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:52692400-52694400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr19:52692400-52694400	Active TSS	Brain Anterior Caudate	brain
46	chr19:52692400-52694400	Active TSS	Duodenum Mucosa	Duodenum
47	chr19:52692400-52694400	Active TSS	Fetal Brain Female	brain
48	chr19:52692400-52694400	Active TSS	Fetal Kidney	kidney
49	chr19:52692400-52694400	Active TSS	Fetal Lung	lung
50	chr19:52692400-52694400	Active TSS	Fetal Stomach	stomach

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