Variant report

Variant	rs450080
Chromosome Location	chr4:2814816-2814817
allele	G/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	MXI1	chr4:2814609-2815076	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:2813394-2815108	GM12892	blood:	n/a	n/a
3	ZNF263	chr4:2813465-2815744	HEK293-T-REx	kidney:	n/a	chr4:2813988-2813997
4	MTA3	chr4:2813221-2816423	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:2813531-2815296	GM18951	blood:	n/a	n/a
6	POLR2A	chr4:2813221-2814866	GM12878	blood:	n/a	n/a
7	EBF1	chr4:2814570-2815126	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr4:2814672-2814819	GM12878	blood:	n/a	n/a
9	POLR2A	chr4:2814569-2815095	HUVEC	blood vessel:	n/a	n/a
10	CHD1	chr4:2814676-2815012	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:2814721-2815097	HUVEC	blood vessel:	n/a	n/a
12	MYC	chr4:2814565-2815036	NB4	blood:	n/a	n/a
13	RUNX3	chr4:2814628-2815430	GM12878	blood:	n/a	n/a
14	FOXM1	chr4:2814623-2814914	GM12878	blood:	n/a	n/a
15	STAT5A	chr4:2814412-2816129	GM12878	blood:	n/a	chr4:2814848-2814856
16	POLR2A	chr4:2814754-2814966	HepG2	liver:	n/a	n/a
17	POLR2A	chr4:2813524-2815110	GM19193	blood:	n/a	n/a
18	POLR2A	chr4:2813573-2815450	GM19099	blood:	n/a	n/a
19	POLR2A	chr4:2814486-2814853	GM12892	blood:	n/a	n/a
20	TCF3	chr4:2814780-2815194	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:2813371-2815082	HUVEC	blood vessel:	n/a	n/a
22	RUNX3	chr4:2814703-2816204	GM12878	blood:	n/a	chr4:2815970-2815987
23	SIN3AK20	chr4:2814763-2814993	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr4:2813516-2815458	GM18505	blood:	n/a	n/a
25	ELF1	chr4:2813378-2815264	GM12878	blood:	n/a	chr4:2813926-2813939 chr4:2814001-2814013 chr4:2813969-2813980 chr4:2815005-2815017
26	POLR2A	chr4:2811919-2815260	HL-60	blood:	n/a	n/a
27	POLR2A	chr4:2813442-2815569	GM12891	blood:	n/a	n/a
28	POLR2A	chr4:2813607-2814820	GM15510	blood:	n/a	n/a
29	MAX	chr4:2813437-2815204	NB4	blood:	n/a	chr4:2814485-2814495 chr4:2814277-2814286

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2811128..2813446-chr4:2813847..2818794,5	MCF-7	breast:

Variant related genes	Relation type
SH3BP2	TF binding region
ENSG00000087266	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10011310	0.81[AMR][1000 genomes]
rs13113803	0.95[CHB][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13137906	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1751848	0.81[CHD][hapmap]
rs1784148	0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[ASN][1000 genomes]
rs1784149	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs2269484	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2269485	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282770	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282771	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3213501	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34993433	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs370470	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs385715	1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs393635	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs397292	1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs402855	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs407770	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs419096	0.90[ASN][1000 genomes]
rs421714	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs422734	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs426192	0.86[EUR][1000 genomes]
rs426904	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs433030	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs445160	0.96[ASN][1000 genomes]
rs6820967	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs743691	0.87[CHB][hapmap]
rs9685721	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948659	chr4:1828867-2815632	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv470002	chr4:2701098-2836628	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878445	chr4:2704046-2831383	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv878447	chr4:2723531-2831383	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv516797	chr4:2723531-2836628	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv878448	chr4:2723531-2846799	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
9	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
10	nsv878449	chr4:2744480-2831383	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv1002517	chr4:2747905-2822017	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv878452	chr4:2789184-2830076	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv461162	chr4:2794320-2846799	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv593436	chr4:2794320-2846799	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs450080	ADD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2803400-2819200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:2809200-2815200	Weak transcription	Fetal Brain Female	brain
3	chr4:2811000-2815200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:2811000-2816000	Enhancers	Brain Substantia Nigra	brain
5	chr4:2811200-2815000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:2811600-2815400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:2811800-2815200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr4:2811800-2819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:2812000-2815400	Weak transcription	Fetal Heart	heart
10	chr4:2812200-2815200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:2812400-2815200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr4:2812600-2815200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:2812600-2815600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:2812800-2815200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr4:2813000-2815200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:2813200-2815200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:2813200-2815400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:2813200-2815400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr4:2813200-2815600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr4:2813200-2815600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr4:2813200-2815600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr4:2813200-2816000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:2813400-2815000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr4:2813400-2815000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr4:2813400-2815200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr4:2813400-2815400	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr4:2813400-2815400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:2813400-2815400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:2813400-2815400	Active TSS	Rectal Smooth Muscle	rectum
30	chr4:2813400-2815400	Flanking Active TSS	HUVEC	blood vessel
31	chr4:2813400-2815600	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr4:2813400-2815800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr4:2813400-2816000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:2813400-2817200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:2813600-2815000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:2813600-2815000	Flanking Active TSS	Right Ventricle	heart
37	chr4:2813600-2815200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:2813600-2815200	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr4:2813600-2815200	Weak transcription	Fetal Brain Male	brain
40	chr4:2813600-2815200	Flanking Active TSS	Fetal Muscle Trunk	muscle
41	chr4:2813600-2815200	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr4:2813600-2815600	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr4:2813600-2815600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:2813600-2815600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:2813800-2815000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:2813800-2815000	Active TSS	Colon Smooth Muscle	Colon
47	chr4:2813800-2815200	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr4:2813800-2815200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr4:2813800-2815200	Transcr. at gene 5' and 3'	Placenta	Placenta
50	chr4:2813800-2815200	Active TSS	Lung	lung

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