Variant report

Variant	rs10405559
Chromosome Location	chr19:52191120-52191121
allele	C/T
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	chr19:52190951-52191397	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr19:52191017-52191791	A549	lung:	n/a	n/a
3	YY1	chr19:52191034-52191338	HCT-116	colon:	n/a	n/a
4	POLR2A	chr19:52190937-52192524	HUVEC	blood vessel:	n/a	n/a
5	REST	chr19:52190820-52192503	A549	lung:	n/a	chr19:52192489-52192502 chr19:52192486-52192499 chr19:52192486-52192499 chr19:52192482-52192502
6	POLR2A	chr19:52190786-52194855	IMR90	lung:	n/a	n/a
7	SP1	chr19:52190731-52192818	HCT-116	colon:	n/a	chr19:52191803-52191812 chr19:52192291-52192302 chr19:52192255-52192266 chr19:52191799-52191813 chr19:52192445-52192459 chr19:52191803-52191813 chr19:52192317-52192328
8	ETS1	chr19:52190932-52191776	A549	lung:	n/a	n/a
9	MAX	chr19:52190747-52194793	A549	lung:	n/a	chr19:52192371-52192381 chr19:52193788-52193797 chr19:52194166-52194176 chr19:52193267-52193277 chr19:52192441-52192451 chr19:52194223-52194233 chr19:52192611-52192621
10	POLR2A	chr19:52190899-52192930	U87	brain:	n/a	n/a
11	MAZ	chr19:52190733-52195005	IMR90	lung:	n/a	chr19:52192371-52192381 chr19:52193788-52193797 chr19:52194166-52194176 chr19:52193267-52193277 chr19:52192441-52192451 chr19:52194223-52194233 chr19:52192611-52192621
12	POLR2A	chr19:52190880-52195017	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr19:52190893-52192936	U87	brain:	n/a	n/a
14	MXI1	chr19:52190804-52195103	SK-N-SH	brain:	n/a	chr19:52193788-52193803
15	POLR2A	chr19:52190868-52194746	PFSK-1	brain:	n/a	n/a
16	REST	chr19:52190718-52193267	H1-neurons	neurons:	n/a	chr19:52192489-52192502 chr19:52192486-52192499 chr19:52192486-52192499 chr19:52192482-52192502
17	POLR2A	chr19:52190880-52192517	U87	brain:	n/a	n/a
18	FOSL2	chr19:52191061-52192493	A549	lung:	n/a	n/a
19	POLR2A	chr19:52191020-52191816	A549	lung:	n/a	n/a
20	NR2F2	chr19:52190988-52191879	MCF-7	breast:	n/a	n/a
21	POLR2A	chr19:52191092-52192906	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr19:52191086-52191370	A549	lung:	n/a	n/a
23	CREB1	chr19:52191013-52191655	A549	lung:	n/a	n/a
24	POLR2A	chr19:52191032-52194338	MCF-7	breast:	n/a	n/a
25	POLR2A	chr19:52190876-52192518	Hela-S3	cervix:	n/a	n/a
26	YY1	chr19:52190996-52191876	A549	lung:	n/a	n/a
27	SIN3AK20	chr19:52191033-52191398	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:52190919-52192517	U87	brain:	n/a	n/a
29	MAX	chr19:52190854-52191918	A549	lung:	n/a	n/a
30	POLR2A	chr19:52190915-52191919	HCT-116	colon:	n/a	n/a
31	E2F6	chr19:52190940-52192581	A549	lung:	n/a	chr19:52192365-52192375 chr19:52192370-52192379
32	ZNF263	chr19:52191114-52194895	HEK293-T-REx	kidney:	n/a	chr19:52194087-52194096 chr19:52192451-52192460 chr19:52193698-52193707 chr19:52194196-52194205 chr19:52192235-52192256 chr19:52194249-52194258 chr19:52193280-52193289 chr19:52192448-52192457 chr19:52194182-52194191
33	KAP1	chr19:52190883-52191732	U2OS	brain:	n/a	n/a
34	SIN3A	chr19:52190956-52194891	H1-hESC	embryonic stem cell:	n/a	chr19:52193317-52193330 chr19:52193832-52193845 chr19:52192489-52192502 chr19:52192592-52192603
35	ZBTB7A	chr19:52191096-52191311	K562	blood:	n/a	n/a
36	TCF12	chr19:52190767-52195036	A549	lung:	n/a	n/a
37	E2F4	chr19:52191039-52191212	MCF10A-Er-Src	breast:	n/a	n/a
38	MAX	chr19:52191119-52191765	Hela-S3	cervix:	n/a	n/a
39	TEAD4	chr19:52190959-52191433	H1-hESC	embryonic stem cell:	n/a	n/a
40	TEAD4	chr19:52191084-52191364	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAZ	chr19:52191031-52194879	K562	blood:	n/a	chr19:52192371-52192381 chr19:52193788-52193797 chr19:52194166-52194176 chr19:52193267-52193277 chr19:52192441-52192451 chr19:52194223-52194233 chr19:52192611-52192621
42	TAF1	chr19:52190903-52194220	A549	lung:	n/a	n/a
43	POLR2A	chr19:52191073-52195667	MCF-7	breast:	n/a	n/a
44	POLR2A	chr19:52191089-52191311	HUVEC	blood vessel:	n/a	n/a
45	SP1	chr19:52190852-52194825	A549	lung:	n/a	chr19:52194193-52194207 chr19:52194168-52194178 chr19:52191803-52191812 chr19:52194161-52194173 chr19:52193770-52193782 chr19:52194167-52194179 chr19:52194168-52194177 chr19:52193856-52193865 chr19:52194258-52194272 chr19:52193694-52193706 chr19:52193266-52193278 chr19:52193073-52193087 chr19:52193855-52193867 chr19:52193767-52193781 chr19:52194162-52194172 chr19:52194394-52194403 chr19:52193772-52193781 chr19:52193278-52193292 chr19:52194167-52194179 chr19:52194162-52194171 chr19:52193852-52193866 chr19:52194393-52194403 chr19:52192291-52192302 chr19:52193771-52193780 chr19:52192255-52192266 chr19:52194158-52194172 chr19:52193855-52193866 chr19:52193695-52193709 chr19:52194161-52194173 chr19:52191799-52191813 chr19:52193770-52193782 chr19:52194169-52194178 chr19:52192445-52192459 chr19:52191803-52191813 chr19:52194164-52194178 chr19:52193694-52193706 chr19:52193203-52193212 chr19:52192317-52192328
46	RCOR1	chr19:52191060-52192853	K562	blood:	n/a	n/a
47	POLR2A	chr19:52191076-52191134	ProgFib	skin:	n/a	n/a
48	POLR2A	chr19:52191075-52191881	MCF-7	breast:	n/a	n/a
49	MAX	chr19:52191110-52192717	SK-N-SH	brain:	n/a	chr19:52192371-52192381 chr19:52192441-52192451 chr19:52192611-52192621
50	CTBP2	chr19:52191102-52195103	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52176167..52177672-chr19:52190052..52191714,2	MCF-7	breast:
2	chr19:52190822..52192582-chr19:52204625..52207087,2	K562	blood:
3	chr19:52163388..52165647-chr19:52189785..52191588,2	MCF-7	breast:
4	chr19:52191055..52194888-chr19:52301421..52305190,4	MCF-7	breast:
5	chr19:51979609..51981467-chr19:52190733..52192569,2	K562	blood:
6	chr19:52189832..52192322-chr19:52204625..52207481,2	K562	blood:
7	chr19:52186234..52189243-chr19:52190984..52192960,3	K562	blood:
8	chr19:52166500..52170915-chr19:52189684..52193816,5	MCF-7	breast:
9	chr19:52190894..52195343-chr19:52204099..52207909,11	MCF-7	breast:
10	chr19:52189901..52192880-chr19:52273718..52275861,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HAS1-1	chr19:52190491-52192335	NONHSAT067461

Variant related genes	Relation type
MIR99B	TF binding region
MIRLET7E	TF binding region
ENSG00000213822	Chromatin interaction
ENSG00000182310	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10408902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28637096	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28727485	0.96[ASN][1000 genomes]
rs56275924	0.82[EUR][1000 genomes]
rs73052807	0.82[EUR][1000 genomes]
rs73052812	0.82[EUR][1000 genomes]
rs73052816	0.82[EUR][1000 genomes]
rs73052817	0.82[EUR][1000 genomes]
rs73052849	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73052856	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73052873	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73052896	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054821	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52190200-52191200	Enhancers	Lung	lung
2	chr19:52190400-52191200	Weak transcription	Ovary	ovary
3	chr19:52190400-52191600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:52190400-52194600	Active TSS	Fetal Brain Female	brain
5	chr19:52190600-52191200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr19:52190600-52191200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:52190600-52191200	Enhancers	Brain Substantia Nigra	brain
8	chr19:52190600-52191600	Flanking Active TSS	NHLF	lung
9	chr19:52190600-52191800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:52190600-52192200	Flanking Active TSS	HMEC	breast
11	chr19:52190800-52191200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr19:52190800-52191200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:52190800-52191200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:52190800-52191200	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr19:52190800-52191200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
16	chr19:52190800-52191200	Flanking Active TSS	Fetal Kidney	kidney
17	chr19:52190800-52191200	Flanking Active TSS	Fetal Stomach	stomach
18	chr19:52190800-52191200	Flanking Active TSS	Left Ventricle	heart
19	chr19:52190800-52191200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
20	chr19:52190800-52191200	Flanking Active TSS	Hela-S3	cervix
21	chr19:52190800-52191400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
22	chr19:52190800-52191400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr19:52190800-52191400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:52190800-52191400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:52190800-52191400	Enhancers	Aorta	Aorta
26	chr19:52190800-52191400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:52190800-52191400	Flanking Active TSS	Fetal Brain Male	brain
28	chr19:52190800-52191400	Flanking Active TSS	NHDF-Ad	bronchial
29	chr19:52190800-52191600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:52190800-52191600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr19:52190800-52191600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:52190800-52191600	Flanking Active TSS	Brain Angular Gyrus	brain
33	chr19:52190800-52191600	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr19:52190800-52191600	Flanking Active TSS	HSMM	muscle
35	chr19:52190800-52191600	Flanking Active TSS	NHEK	skin
36	chr19:52190800-52191800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:52190800-52191800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:52190800-52191800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr19:52190800-52191800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:52190800-52191800	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr19:52190800-52191800	Flanking Active TSS	Right Ventricle	heart
42	chr19:52190800-52191800	Flanking Active TSS	K562	blood
43	chr19:52190800-52192000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:52190800-52192000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:52190800-52192000	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr19:52190800-52192000	Active TSS	Right Atrium	heart
47	chr19:52190800-52192200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:52190800-52192200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:52190800-52192200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr19:52190800-52192200	Flanking Active TSS	Fetal Heart	heart

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