Variant report

Variant	rs12461641
Chromosome Location	chr19:52191534-52191535
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	chr19:52191017-52191791	A549	lung:	n/a	n/a
2	TCF12	chr19:52191382-52191838	A549	lung:	n/a	n/a
3	POLR2A	chr19:52190937-52192524	HUVEC	blood vessel:	n/a	n/a
4	JUND	chr19:52191158-52191598	K562	blood:	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	MYC	chr19:52191462-52191662	MCF10A-Er-Src	breast:	n/a	n/a
8	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
9	TAF1	chr19:52191155-52192632	H1-neurons	neurons:	n/a	n/a
10	ZKSCAN1	chr19:52191276-52191661	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:52191161-52194568	HUVEC	blood vessel:	n/a	n/a
12	ETS1	chr19:52190932-52191776	A549	lung:	n/a	n/a
13	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
14	POLR2A	chr19:52190899-52192930	U87	brain:	n/a	n/a
15	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
16	POLR2A	chr19:52190880-52195017	PFSK-1	brain:	n/a	n/a
17	NR2F2	chr19:52191395-52191976	K562	blood:	n/a	n/a
18	POLR2A	chr19:52190893-52192936	U87	brain:	n/a	n/a
19	UBTF	chr19:52191202-52193378	K562	blood:	n/a	n/a
20	MXI1	chr19:52190804-52195103	SK-N-SH	brain:	n/a	chr19:52193788-52193803
21	POLR2A	chr19:52191380-52191771	A549	lung:	n/a	n/a
22	GTF2F1	chr19:52191346-52191542	Hela-S3	cervix:	n/a	n/a
23	MXI1	chr19:52191427-52191694	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:52190868-52194746	PFSK-1	brain:	n/a	n/a
25	REST	chr19:52190718-52193267	H1-neurons	neurons:	n/a	chr19:52192489-52192502 chr19:52192486-52192499 chr19:52192486-52192499 chr19:52192482-52192502
26	E2F4	chr19:52191484-52191814	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr19:52190880-52192517	U87	brain:	n/a	n/a
28	RFX5	chr19:52191223-52191753	Hela-S3	cervix:	n/a	n/a
29	FOSL2	chr19:52191061-52192493	A549	lung:	n/a	n/a
30	POLR2A	chr19:52191020-52191816	A549	lung:	n/a	n/a
31	NR2F2	chr19:52190988-52191879	MCF-7	breast:	n/a	n/a
32	POLR2A	chr19:52191092-52192906	H1-neurons	neurons:	n/a	n/a
33	CREB1	chr19:52191013-52191655	A549	lung:	n/a	n/a
34	POLR2A	chr19:52191032-52194338	MCF-7	breast:	n/a	n/a
35	POLR2A	chr19:52190876-52192518	Hela-S3	cervix:	n/a	n/a
36	YY1	chr19:52190996-52191876	A549	lung:	n/a	n/a
37	POLR2A	chr19:52190919-52192517	U87	brain:	n/a	n/a
38	ZBTB33	chr19:52191329-52191786	A549	lung:	n/a	n/a
39	POLR2A	chr19:52191279-52191905	HepG2	liver:	n/a	n/a
40	MAX	chr19:52190854-52191918	A549	lung:	n/a	n/a
41	MAX	chr19:52191476-52191550	K562	blood:	n/a	n/a
42	POLR2A	chr19:52190915-52191919	HCT-116	colon:	n/a	n/a
43	EP300	chr19:52191504-52194723	A549	lung:	n/a	chr19:52192452-52192468
44	SIN3AK20	chr19:52191210-52191687	PFSK-1	brain:	n/a	n/a
45	UBTF	chr19:52191298-52191590	K562	blood:	n/a	n/a
46	POLR2A	chr19:52191223-52191752	A549	lung:	n/a	n/a
47	STAT3	chr19:52191341-52191607	MCF10A-Er-Src	breast:	n/a	n/a
48	E2F6	chr19:52190940-52192581	A549	lung:	n/a	chr19:52192365-52192375 chr19:52192370-52192379
49	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
50	KAP1	chr19:52190883-52191732	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52191310..52193737-chr19:54959271..54961784,2	MCF-7	breast:
2	chr19:52176167..52177672-chr19:52190052..52191714,2	MCF-7	breast:
3	chr19:52191235..52193231-chr19:52302966..52304607,2	MCF-7	breast:
4	chr19:52190822..52192582-chr19:52204625..52207087,2	K562	blood:
5	chr19:52163388..52165647-chr19:52189785..52191588,2	MCF-7	breast:
6	chr19:52191055..52194888-chr19:52301421..52305190,4	MCF-7	breast:
7	chr19:51979609..51981467-chr19:52190733..52192569,2	K562	blood:
8	chr19:52189832..52192322-chr19:52204625..52207481,2	K562	blood:
9	chr19:52186234..52189243-chr19:52190984..52192960,3	K562	blood:
10	chr19:52166500..52170915-chr19:52189684..52193816,5	MCF-7	breast:
11	chr19:52190894..52195343-chr19:52204099..52207909,11	MCF-7	breast:
12	chr19:52171940..52173838-chr19:52191282..52193363,2	MCF-7	breast:
13	chr19:52189901..52192880-chr19:52273718..52275861,2	MCF-7	breast:
14	chr19:52191148..52193451-chr19:52208033..52210074,2	MCF-7	breast:

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

Variant related genes	Relation type
MIRLET7E	TF binding region
MIR125A	TF binding region
MIR99B	TF binding region
ENSG00000182310	Chromatin interaction
ENSG00000238486	Chromatin interaction
ENSG00000167615	Chromatin interaction
ENSG00000226696	Chromatin interaction
ENSG00000213822	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11084104	0.87[ASN][1000 genomes]
rs12459728	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12460218	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12462216	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12462233	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12462291	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1868941	0.92[ASN][1000 genomes]
rs28616281	0.87[ASN][1000 genomes]
rs34480258	0.83[ASN][1000 genomes]
rs4802839	0.87[ASN][1000 genomes]
rs61493009	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7255206	0.92[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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52190400-52191600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr19:52190400-52194600	Active TSS	Fetal Brain Female	brain
3	chr19:52190600-52191600	Flanking Active TSS	NHLF	lung
4	chr19:52190600-52191800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:52190600-52192200	Flanking Active TSS	HMEC	breast
6	chr19:52190800-52191600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:52190800-52191600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr19:52190800-52191600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:52190800-52191600	Flanking Active TSS	Brain Angular Gyrus	brain
10	chr19:52190800-52191600	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr19:52190800-52191600	Flanking Active TSS	HSMM	muscle
12	chr19:52190800-52191600	Flanking Active TSS	NHEK	skin
13	chr19:52190800-52191800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:52190800-52191800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:52190800-52191800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr19:52190800-52191800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:52190800-52191800	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr19:52190800-52191800	Flanking Active TSS	Right Ventricle	heart
19	chr19:52190800-52191800	Flanking Active TSS	K562	blood
20	chr19:52190800-52192000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:52190800-52192000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:52190800-52192000	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr19:52190800-52192000	Active TSS	Right Atrium	heart
24	chr19:52190800-52192200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:52190800-52192200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:52190800-52192200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr19:52190800-52192200	Flanking Active TSS	Fetal Heart	heart
28	chr19:52190800-52192200	Flanking Active TSS	Fetal Lung	lung
29	chr19:52190800-52192200	Flanking Active TSS	Placenta	Placenta
30	chr19:52190800-52192200	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr19:52190800-52192200	Flanking Active TSS	Osteobl	bone
32	chr19:52190800-52194400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:52190800-52194400	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr19:52190800-52194800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:52190800-52194800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:52190800-52195000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr19:52190800-52195000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:52190800-52195200	Active TSS	H9 Cell Line	embryonic stem cell
39	chr19:52191000-52191600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr19:52191000-52191600	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr19:52191000-52191600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
42	chr19:52191000-52191800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:52191000-52191800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
44	chr19:52191000-52191800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
45	chr19:52191000-52191800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
46	chr19:52191000-52191800	Flanking Active TSS	NH-A	brain
47	chr19:52191000-52192000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:52191000-52192000	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr19:52191000-52192000	Flanking Active TSS	Fetal Muscle Trunk	muscle
50	chr19:52191000-52192000	Bivalent Enhancer	Stomach Mucosa	stomach

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