Variant report

Variant	rs1281123
Chromosome Location	chr4:8203372-8203373
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	PAX5	chr4:8203009-8203688	GM12878	blood:	n/a	n/a
2	SPI1	chr4:8203094-8203692	HL-60	blood:	n/a	n/a
3	POLR2A	chr4:8200369-8205269	GM12878	blood:	n/a	n/a
4	CTCF	chr4:8203240-8203390	GM12872	blood:	n/a	chr4:8203280-8203293 chr4:8203284-8203293
5	RELA	chr4:8203238-8203641	GM12892	blood:	n/a	chr4:8203445-8203454 chr4:8203445-8203454
6	POLR2A	chr4:8201586-8203464	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr4:8202868-8203599	Raji	blood:	n/a	n/a
8	RELA	chr4:8202830-8203901	GM19193	blood:	n/a	chr4:8203445-8203454 chr4:8203445-8203454
9	SP1	chr4:8203141-8203591	GM12878	blood:	n/a	chr4:8203352-8203366
10	RCOR1	chr4:8201768-8203775	GM12878	blood:	n/a	n/a
11	SPI1	chr4:8203217-8203644	GM12891	blood:	n/a	n/a
12	POLR2A	chr4:8203110-8203652	GM12891	blood:	n/a	n/a
13	POLR2A	chr4:8200443-8205116	GM18505	blood:	n/a	n/a
14	ZEB1	chr4:8203178-8203555	GM12878	blood:	n/a	n/a
15	BCLAF1	chr4:8203140-8203628	GM12878	blood:	n/a	chr4:8203444-8203453
16	SPI1	chr4:8203230-8203473	GM12878	blood:	n/a	n/a
17	POLR2A	chr4:8201774-8204219	GM12878	blood:	n/a	n/a
18	ATF2	chr4:8203146-8203570	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:8200122-8204378	GM18526	blood:	n/a	n/a
20	STAT1	chr4:8202554-8203563	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:8200506-8204225	GM19193	blood:	n/a	n/a
22	RELA	chr4:8203103-8203654	GM15510	blood:	n/a	chr4:8203445-8203454 chr4:8203445-8203454
23	POLR2A	chr4:8200695-8203509	HUVEC	blood vessel:	n/a	n/a
24	STAT5A	chr4:8202686-8203681	GM12878	blood:	n/a	n/a
25	EBF1	chr4:8203130-8204210	GM12878	blood:	n/a	n/a
26	TAF1	chr4:8203133-8203571	GM12878	blood:	n/a	n/a
27	POLR2A	chr4:8200565-8203402	PFSK-1	brain:	n/a	n/a
28	RELA	chr4:8202997-8203726	GM19099	blood:	n/a	chr4:8203445-8203454 chr4:8203445-8203454
29	TCF12	chr4:8203097-8203621	GM12878	blood:	n/a	n/a
30	ZNF143	chr4:8203090-8203564	GM12878	blood:	n/a	n/a
31	SMC3	chr4:8203192-8203853	GM12878	blood:	n/a	n/a
32	CHD2	chr4:8202934-8204937	GM12878	blood:	n/a	chr4:8204641-8204651
33	MYC	chr4:8203162-8203518	NB4	blood:	n/a	n/a
34	RUNX3	chr4:8202394-8203747	GM12878	blood:	n/a	n/a
35	SPI1	chr4:8203188-8203560	GM12891	blood:	n/a	n/a
36	EBF1	chr4:8203150-8203646	GM12878	blood:	n/a	n/a
37	CTCF	chr4:8203272-8203543	GM12878	blood:	n/a	chr4:8203280-8203293 chr4:8203284-8203293
38	POLR2A	chr4:8203124-8203606	GM12892	blood:	n/a	n/a
39	RELA	chr4:8202897-8203620	GM18526	blood:	n/a	chr4:8203445-8203454 chr4:8203445-8203454
40	POLR2A	chr4:8203070-8203701	GM12892	blood:	n/a	n/a
41	POLR2A	chr4:8200430-8203861	HUVEC	blood vessel:	n/a	n/a
42	MAZ	chr4:8201965-8205055	GM12878	blood:	n/a	chr4:8203087-8203096
43	POLR2A	chr4:8202878-8203473	HUVEC	blood vessel:	n/a	n/a
44	STAT5A	chr4:8203132-8203518	GM12878	blood:	n/a	n/a
45	WRNIP1	chr4:8201617-8204724	GM12878	blood:	n/a	n/a
46	RELA	chr4:8202884-8203805	GM10847	blood:	n/a	chr4:8203445-8203454 chr4:8203445-8203454
47	RFX5	chr4:8203355-8203579	GM12878	blood:	n/a	n/a
48	SPI1	chr4:8203048-8204327	GM12878	blood:	n/a	n/a
49	MTA3	chr4:8200020-8205097	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:8200473-8203690	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:8202937..8205415-chr4:8232393..8234006,2	K562	blood:
2	chr4:8199393..8202510-chr4:8203198..8206188,4	MCF-7	breast:
3	chr4:8181697..8186152-chr4:8199354..8203571,7	MCF-7	breast:
4	chr4:8158369..8164233-chr4:8200767..8204083,4	MCF-7	breast:
5	chr4:8199821..8202591-chr4:8203028..8206014,3	K562	blood:

Variant related genes	Relation type
SH3TC1	TF binding region
ENSG00000125089	Chromatin interaction
ENSG00000163995	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1078701	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1281114	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1281115	1.00[CEU][hapmap]
rs1281118	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1281119	0.92[EUR][1000 genomes]
rs1281120	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1678261	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1678262	1.00[CEU][hapmap]
rs1678310	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3115217	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv878591	chr4:8063501-8207083	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1010809	chr4:8097627-8292324	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv878593	chr4:8125788-8233341	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv461216	chr4:8154534-8276411	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv593626	chr4:8154534-8276411	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv878594	chr4:8154534-8286916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	20 gene(s)	inside rSNPs	diseases
8	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv470012	chr4:8171401-8233341	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv878596	chr4:8171401-8254784	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv878597	chr4:8171401-8294196	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
12	nsv829853	chr4:8172065-8320868	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
13	nsv869928	chr4:8195069-8214848	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv878598	chr4:8195705-8254784	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv878599	chr4:8195705-8293398	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	esv2763338	chr4:8199091-8260812	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	esv1831794	chr4:8199833-8233341	Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	nsv593627	chr4:8202211-8311043	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8195800-8204200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:8200000-8204000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr4:8200000-8206000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:8200200-8203800	Active TSS	Rectal Smooth Muscle	rectum
5	chr4:8200200-8204000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:8200200-8204000	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr4:8200200-8204800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr4:8200200-8205800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:8200400-8203600	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr4:8200400-8203600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr4:8200400-8203600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:8200400-8204000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:8200400-8204000	Active TSS	Brain Anterior Caudate	brain
14	chr4:8200400-8204400	Flanking Active TSS	Fetal Thymus	thymus
15	chr4:8200600-8203400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:8200600-8203600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr4:8200600-8203800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr4:8200600-8204000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:8200600-8204000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:8200600-8205200	Flanking Active TSS	Dnd41	blood
21	chr4:8200800-8203400	Flanking Active TSS	Placenta	Placenta
22	chr4:8200800-8203800	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr4:8201000-8203400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr4:8201200-8204600	Active TSS	Brain Hippocampus Middle	brain
25	chr4:8201400-8203400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:8201400-8203400	Flanking Active TSS	Fetal Intestine Large	intestine
27	chr4:8201400-8203800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr4:8201400-8203800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr4:8201600-8203400	Enhancers	NH-A	brain
30	chr4:8201800-8203400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:8201800-8204600	Flanking Active TSS	Liver	Liver
32	chr4:8201800-8204600	Flanking Active TSS	GM12878-XiMat	blood
33	chr4:8201800-8204800	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr4:8202000-8203400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:8202000-8204000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:8202000-8204000	Flanking Active TSS	HUVEC	blood vessel
37	chr4:8202000-8204800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr4:8202200-8203600	Transcr. at gene 5' and 3'	NHEK	skin
39	chr4:8202200-8204400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
40	chr4:8202400-8203400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr4:8202400-8203400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr4:8202400-8203800	Active TSS	Thymus	Thymus
43	chr4:8202400-8204200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:8202400-8205400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:8202600-8203400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:8202600-8203400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:8202600-8203400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:8202600-8203400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr4:8202600-8203600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:8202600-8203600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood

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