Variant report

Variant	rs41275794
Chromosome Location	chr19:52196409-52196410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:52196384-52196447	K562	blood:	n/a	n/a
2	POLR2A	chr19:52196227-52197752	PFSK-1	brain:	n/a	n/a
3	NR2F2	chr19:52196367-52197041	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52196159..52199511-chr19:52202868..52206043,4	K562	blood:

Variant related genes	Relation type
MIR125A	TF binding region
ENSG00000273318	TF binding region
SPACA6P	TF binding region
ENSG00000182310	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs45475696	1.00[AFR][1000 genomes]
rs45580238	1.00[AFR][1000 genomes]
rs61736495	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
2	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
3	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
4	nsv1064914	chr19:52103914-52231564	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	529 gene(s)	inside rSNPs	diseases
5	nsv544052	chr19:52103914-52271247	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	531 gene(s)	inside rSNPs	diseases
6	nsv1056825	chr19:52103914-52359815	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
7	nsv544053	chr19:52103914-52359815	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
8	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
9	esv1843680	chr19:52131510-52211749	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
10	nsv1066046	chr19:52147399-52271247	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
11	nsv544054	chr19:52147399-52271247	Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
12	nsv912296	chr19:52182363-52231032	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	518 gene(s)	inside rSNPs	diseases
13	nsv915725	chr19:52184488-52439676	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
14	nsv9742	chr19:52187538-52221742	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	517 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52194200-52205400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52194600-52205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr19:52194600-52207000	Weak transcription	Psoas Muscle	Psoas
4	chr19:52194800-52196600	Weak transcription	Aorta	Aorta
5	chr19:52194800-52196800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:52194800-52198600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:52194800-52204600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:52194800-52205200	Weak transcription	Stomach Mucosa	stomach
9	chr19:52195000-52197000	Enhancers	Fetal Brain Male	brain
10	chr19:52195000-52198000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:52195000-52198000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr19:52195000-52205600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:52195000-52205600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr19:52195000-52205800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr19:52195000-52205800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:52195200-52199000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:52195200-52205800	Weak transcription	Primary T cells from cord blood	blood
18	chr19:52195400-52196600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr19:52195400-52196600	Weak transcription	Esophagus	oesophagus
20	chr19:52195400-52196600	Enhancers	Left Ventricle	heart
21	chr19:52195400-52196600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr19:52195400-52197000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:52195400-52197600	Weak transcription	HSMMtube	muscle
24	chr19:52195400-52201400	Weak transcription	Liver	Liver
25	chr19:52195400-52204600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr19:52195400-52207200	Weak transcription	Hela-S3	cervix
27	chr19:52195600-52196600	Weak transcription	NHDF-Ad	bronchial
28	chr19:52195600-52197000	Genic enhancers	Fetal Muscle Trunk	muscle
29	chr19:52195600-52197000	Genic enhancers	Placenta Amnion	Placenta Amnion
30	chr19:52195600-52198000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:52195600-52198000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:52195600-52198600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:52195600-52203200	Strong transcription	Fetal Intestine Small	intestine
34	chr19:52195600-52204600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr19:52195600-52204800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr19:52195800-52196600	Genic enhancers	HUVEC	blood vessel
37	chr19:52195800-52196800	Enhancers	K562	blood
38	chr19:52195800-52197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr19:52195800-52197600	Strong transcription	Lung	lung
40	chr19:52195800-52197800	Enhancers	Right Atrium	heart
41	chr19:52195800-52198000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr19:52195800-52198200	Genic enhancers	Placenta	Placenta
43	chr19:52195800-52198800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:52195800-52204600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr19:52196000-52196600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:52196000-52196800	Enhancers	HepG2	liver
47	chr19:52196000-52197000	Genic enhancers	Brain Hippocampus Middle	brain
48	chr19:52196000-52197200	Genic enhancers	HMEC	breast
49	chr19:52196000-52197400	Weak transcription	Brain Angular Gyrus	brain
50	chr19:52196000-52197600	Weak transcription	HSMM	muscle

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