Variant report

Variant	rs617073
Chromosome Location	chr19:56180968-56180969
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56177320-56182238	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr19:56180660-56181129	A549	lung:	n/a	n/a
3	POLR2A	chr19:56180603-56181168	GM12892	blood:	n/a	n/a
4	CTCF	chr19:56180759-56181047	T-47D	breast:	n/a	n/a
5	POLR2A	chr19:56180729-56181126	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:56180425-56181312	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:56180934-56180985	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr19:56180750-56181033	A549	lung:	n/a	n/a
9	POLR2A	chr19:56180761-56181101	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:56179437-56183102	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:56180664-56183041	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:56180416-56181347	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:56180904-56181115	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr19:56177383-56182464	GM12892	blood:	n/a	n/a
15	POLR2A	chr19:56180025-56183224	HL-60	blood:	n/a	n/a
16	POLR2A	chr19:56179314-56181941	K562	blood:	n/a	n/a
17	POLR2A	chr19:56180666-56181170	GM12891	blood:	n/a	n/a
18	POLR2A	chr19:56180731-56181301	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr19:56180627-56183153	K562	blood:	n/a	n/a
20	POLR2A	chr19:56180800-56182160	HepG2	liver:	n/a	n/a
21	POLR2A	chr19:56177227-56182460	K562	blood:	n/a	n/a
22	POLR2A	chr19:56180637-56182430	GM12892	blood:	n/a	n/a
23	POLR2A	chr19:56180652-56182438	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:56180532-56181062	GM12891	blood:	n/a	n/a
25	POLR2A	chr19:56180514-56181054	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:56180772-56182630	K562	blood:	n/a	n/a
27	POLR2A	chr19:56177574-56182562	GM12892	blood:	n/a	n/a
28	POLR2A	chr19:56177312-56183116	A549	lung:	n/a	n/a
29	POLR2A	chr19:56180720-56181296	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:56179427-56183202	HepG2	liver:	n/a	n/a
31	POLR2A	chr19:56177127-56183356	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr19:56180390-56182758	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56152350..56154364-chr19:56178163..56180977,2	MCF-7	breast:
2	chr19:56164975..56168855-chr19:56176069..56182259,9	MCF-7	breast:
3	chr19:56178386..56181077-chr19:56181420..56183133,2	MCF-7	breast:
4	chr19:56178755..56181299-chr19:59055789..59058317,2	MCF-7	breast:
5	chr19:55917418..55919506-chr19:56180430..56182148,2	K562	blood:
6	chr19:56143909..56147540-chr19:56180767..56182811,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267096	TF binding region
ENSG00000267096	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000130726	Chromatin interaction
ENSG00000171425	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10402618	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10403866	0.89[ASN][1000 genomes]
rs10408613	0.86[ASN][1000 genomes]
rs10410404	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10410802	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10410886	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10412050	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10415521	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10417539	0.89[ASN][1000 genomes]
rs10421319	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11882031	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280255	0.87[ASN][1000 genomes]
rs2287791	0.91[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28375493	0.82[ASN][1000 genomes]
rs28385383	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28595590	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28668166	0.89[ASN][1000 genomes]
rs310437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs310441	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310472	0.82[ASN][1000 genomes]
rs3745446	0.88[ASN][1000 genomes]
rs4801526	0.88[ASN][1000 genomes]
rs523509	0.93[ASN][1000 genomes]
rs575274	0.84[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap]
rs57544196	0.89[ASN][1000 genomes]
rs584405	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58490076	0.86[ASN][1000 genomes]
rs60873246	0.87[ASN][1000 genomes]
rs610811	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs648651	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs681804	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256441	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73613281	0.89[ASN][1000 genomes]
rs8100143	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8104242	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8109983	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	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
7	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
8	esv3349569	chr19:56179960-56182791	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs617073	VCAM1	trans	brain	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56169600-56181600	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:56170000-56181600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:56170000-56181600	Strong transcription	Aorta	Aorta
4	chr19:56170000-56181800	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr19:56170000-56184800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:56170200-56181600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr19:56170200-56181800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:56170200-56182200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:56170200-56182400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:56170200-56182400	Strong transcription	Rectal Smooth Muscle	rectum
11	chr19:56170200-56184000	Strong transcription	Primary T cells from cord blood	blood
12	chr19:56170200-56185200	Strong transcription	Fetal Thymus	thymus
13	chr19:56170200-56185400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr19:56170200-56185800	Strong transcription	Fetal Stomach	stomach
15	chr19:56170400-56181600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:56170400-56181600	Strong transcription	Fetal Muscle Leg	muscle
17	chr19:56170400-56182200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:56170400-56183000	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:56170400-56185600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:56170400-56185800	Strong transcription	Fetal Brain Female	brain
21	chr19:56170600-56181600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr19:56170600-56181600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:56170600-56181600	Strong transcription	Thymus	Thymus
24	chr19:56170600-56182400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:56170600-56182400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr19:56170800-56181600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:56170800-56181600	Strong transcription	Colonic Mucosa	Colon
28	chr19:56170800-56182600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:56170800-56182800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:56170800-56185400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr19:56170800-56185800	Weak transcription	Psoas Muscle	Psoas
32	chr19:56170800-56186000	Weak transcription	Right Atrium	heart
33	chr19:56171000-56181400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
34	chr19:56171000-56181600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:56171000-56181600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr19:56171000-56181600	Strong transcription	Left Ventricle	heart
37	chr19:56171000-56181800	Strong transcription	Brain Germinal Matrix	brain
38	chr19:56171000-56182000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:56171000-56182800	Strong transcription	NHLF	lung
40	chr19:56171200-56182600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:56171200-56183000	Strong transcription	Primary B cells from cord blood	blood
42	chr19:56171200-56184600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:56171400-56181400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr19:56171400-56181600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:56171400-56181600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:56171400-56181600	Strong transcription	Adipose Nuclei	Adipose
47	chr19:56171400-56181600	Strong transcription	Liver	Liver
48	chr19:56171400-56181600	Strong transcription	Brain Cingulate Gyrus	brain
49	chr19:56171400-56181600	Strong transcription	Brain Hippocampus Middle	brain
50	chr19:56171400-56181600	Strong transcription	Brain Inferior Temporal Lobe	brain

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