Variant report

Variant	rs637788
Chromosome Location	chr19:56168181-56168182
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	chr19:56168100-56168375	MCF-7	breast:	n/a	n/a
2	MAX	chr19:56168079-56168190	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:56164855-56168213	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:56168112-56168822	Hela-S3	cervix:	n/a	n/a
5	HCFC1	chr19:56164938-56168188	Hela-S3	cervix:	n/a	n/a
6	HEY1	chr19:56167387-56168350	K562	blood:	n/a	n/a
7	POLR2A	chr19:56168119-56168815	HepG2	liver:	n/a	n/a
8	CTCF	chr19:56168060-56168210	HAc	cerebellar:	n/a	n/a
9	MYC	chr19:56167880-56169282	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr19:56168100-56168250	GM12875	blood:	n/a	n/a
11	MAX	chr19:56168061-56169062	GM12878	blood:	n/a	n/a
12	MYC	chr19:56167951-56168574	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr19:56164941-56169020	GM12878	blood:	n/a	n/a
14	MTA3	chr19:56167947-56168817	GM12878	blood:	n/a	n/a
15	WRNIP1	chr19:56166793-56170333	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:56164851-56170437	PANC-1	pancreas:	n/a	n/a
17	IRF1	chr19:56164969-56168457	K562	blood:	n/a	chr19:56165607-56165620 chr19:56165602-56165619 chr19:56165700-56165720 chr19:56165608-56165618 chr19:56166942-56166956 chr19:56165608-56165622 chr19:56165604-56165618 chr19:56165606-56165626 chr19:56165607-56165618
18	MAX	chr19:56167934-56168361	K562	blood:	n/a	n/a
19	REST	chr19:56166301-56168198	A549	lung:	n/a	chr19:56166748-56166761 chr19:56166745-56166758 chr19:56167749-56167769
20	POLR2A	chr19:56167935-56168674	HepG2	liver:	n/a	n/a
21	POLR2A	chr19:56164956-56169503	K562	blood:	n/a	n/a
22	POLR2A	chr19:56167955-56169676	GM12878	blood:	n/a	n/a
23	MYC	chr19:56164961-56168359	K562	blood:	n/a	chr19:56166757-56166772 chr19:56167157-56167173 chr19:56166761-56166771 chr19:56166756-56166775 chr19:56166759-56166774 chr19:56166762-56166771 chr19:56166759-56166768 chr19:56166760-56166770 chr19:56166761-56166770
24	CEBPB	chr19:56168153-56168422	K562	blood:	n/a	n/a
25	RUNX3	chr19:56167921-56168359	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:56166277-56169272	GM12878	blood:	n/a	n/a
27	STAT1	chr19:56168168-56168599	GM12878	blood:	n/a	chr19:56168527-56168538
28	PML	chr19:56168096-56168724	GM12878	blood:	n/a	n/a
29	CHD1	chr19:56167921-56168644	GM12878	blood:	n/a	n/a
30	TBL1XR1	chr19:56167709-56168182	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:56164926-56168745	GM12891	blood:	n/a	n/a
32	RUNX3	chr19:56168002-56168793	GM12878	blood:	n/a	n/a
33	JUN	chr19:56164949-56168739	K562	blood:	n/a	chr19:56165258-56165272 chr19:56166577-56166586
34	POLR2A	chr19:56164827-56168951	SK-N-MC	brain:	n/a	n/a
35	CHD1	chr19:56166327-56168561	IMR90	lung:	n/a	n/a
36	CTCF	chr19:56168100-56168250	GM12872	blood:	n/a	n/a
37	MXI1	chr19:56164856-56169392	SK-N-SH	brain:	n/a	chr19:56165279-56165294 chr19:56166760-56166769 chr19:56165281-56165296 chr19:56166762-56166771
38	POLR2A	chr19:56168085-56168978	GM12892	blood:	n/a	n/a
39	POLR2A	chr19:56167876-56168340	PFSK-1	brain:	n/a	n/a
40	MXI1	chr19:56167921-56169134	GM12878	blood:	n/a	n/a
41	MAFK	chr19:56167941-56168466	K562	blood:	n/a	n/a
42	POLR2A	chr19:56167974-56169193	GM12892	blood:	n/a	n/a
43	STAT3	chr19:56168127-56168401	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr19:56167830-56168325	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:54974496..54976652-chr19:56167995..56170937,2	MCF-7	breast:
2	chr19:56164975..56168855-chr19:56176069..56182259,9	MCF-7	breast:
3	chr19:56165463..56168899-chr19:56631045..56633379,3	K562	blood:
4	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
5	chr19:56167793..56169420-chr19:56762867..56764897,2	K562	blood:
6	chr19:56165703..56169980-chr19:56194386..56196896,5	MCF-7	breast:
7	chr19:55627421..55629071-chr19:56166474..56168541,2	MCF-7	breast:
8	chr19:55850613..55852119-chr19:56166654..56168818,2	K562	blood:
9	chr19:56134221..56137618-chr19:56162633..56168532,10	K562	blood:

Variant related genes	Relation type
U2AF2	TF binding region
ENSG00000133247	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000182909	Chromatin interaction
ENSG00000211571	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000267096	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11545669	1.00[ASN][1000 genomes]
rs310438	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310439	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310442	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310443	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310444	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310464	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs310465	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs310467	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs310470	0.89[EUR][1000 genomes]
rs310471	0.89[EUR][1000 genomes]
rs310474	0.89[EUR][1000 genomes]
rs504003	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs507498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520125	1.00[CHB][hapmap]
rs522669	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs537728	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553947	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[YRI][hapmap]
rs57063593	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581023	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600106	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612211	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[EUR][1000 genomes]
rs630491	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636466	0.89[EUR][1000 genomes]
rs636467	0.89[EUR][1000 genomes]
rs644230	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[EUR][1000 genomes]
rs679577	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680444	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246799	0.89[EUR][1000 genomes]
rs889091	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
5	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
7	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 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	chr19:56163400-56168200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:56164400-56168400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:56164800-56168200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:56164800-56168200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr19:56165000-56168200	Active TSS	Fetal Intestine Small	intestine
6	chr19:56165200-56168200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:56165600-56168200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:56166400-56168800	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr19:56166600-56168800	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr19:56166600-56168800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:56166800-56169400	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr19:56167000-56168200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr19:56167000-56168400	Flanking Active TSS	Fetal Brain Male	brain
14	chr19:56167000-56168400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr19:56167000-56168600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:56167000-56169000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr19:56167000-56169200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:56167000-56169200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
19	chr19:56167000-56169200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr19:56167000-56169200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr19:56167000-56169200	Transcr. at gene 5' and 3'	A549	lung
22	chr19:56167000-56169400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr19:56167000-56169400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr19:56167000-56169400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr19:56167000-56169400	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr19:56167000-56169400	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr19:56167000-56169400	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr19:56167000-56169400	Transcr. at gene 5' and 3'	K562	blood
29	chr19:56167000-56170200	Transcr. at gene 5' and 3'	Dnd41	blood
30	chr19:56167200-56168200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
31	chr19:56167200-56168200	Flanking Active TSS	Placenta	Placenta
32	chr19:56167200-56168400	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr19:56167200-56168600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
34	chr19:56167200-56168600	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
35	chr19:56167200-56168800	Flanking Active TSS	Brain Substantia Nigra	brain
36	chr19:56167200-56169000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:56167200-56169000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:56167200-56169000	Flanking Active TSS	Colonic Mucosa	Colon
39	chr19:56167200-56169000	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr19:56167200-56169000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
41	chr19:56167200-56169000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr19:56167200-56169200	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr19:56167200-56169200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr19:56167200-56169200	Transcr. at gene 5' and 3'	NHEK	skin
45	chr19:56167200-56169400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr19:56167200-56169400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr19:56167200-56169400	Flanking Active TSS	HUVEC	blood vessel
48	chr19:56167200-56169400	Flanking Active TSS	NH-A	brain
49	chr19:56167200-56169400	Flanking Active TSS	Osteobl	bone
50	chr19:56167200-56169600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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