Variant report

Variant	rs4670961
Chromosome Location	chr2:40008428-40008429
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	IRF1	chr2:40008411-40008768	K562	blood:	n/a	chr2:40008625-40008638 chr2:40008625-40008636 chr2:40008625-40008638 chr2:40008624-40008638 chr2:40008620-40008637 chr2:40008626-40008640 chr2:40008623-40008637 chr2:40008625-40008638 chr2:40008625-40008639 chr2:40008624-40008637 chr2:40008623-40008637 chr2:40008624-40008634 chr2:40008624-40008635
2	RCOR1	chr2:40007846-40008600	K562	blood:	n/a	n/a
3	EP300	chr2:40007880-40008672	K562	blood:	n/a	n/a
4	MAX	chr2:40007967-40008616	K562	blood:	n/a	n/a
5	MYC	chr2:40008130-40008772	K562	blood:	n/a	n/a
6	POLR2A	chr2:40007977-40008430	K562	blood:	n/a	n/a
7	MAFK	chr2:40007871-40008634	K562	blood:	n/a	chr2:40008378-40008394
8	HMGN3	chr2:40007929-40008523	K562	blood:	n/a	n/a
9	ARID3A	chr2:40008059-40008584	K562	blood:	n/a	n/a
10	HCFC1	chr2:40007954-40008673	K562	blood:	n/a	n/a
11	KAP1	chr2:40007806-40008461	HEK293	kidney:	n/a	n/a
12	MAZ	chr2:40007932-40008652	K562	blood:	n/a	n/a
13	ZMIZ1	chr2:40008032-40008528	K562	blood:	n/a	n/a
14	CHD2	chr2:40008014-40008754	K562	blood:	n/a	n/a
15	RCOR1	chr2:40007780-40008788	K562	blood:	n/a	n/a
16	JUN	chr2:40008373-40008742	K562	blood:	n/a	n/a
17	MAFK	chr2:40008208-40008606	HepG2	liver:	n/a	chr2:40008378-40008394
18	MAX	chr2:40007662-40008752	NB4	blood:	n/a	n/a
19	JUND	chr2:40007870-40008701	K562	blood:	n/a	chr2:40008030-40008041
20	TEAD4	chr2:40007722-40008790	K562	blood:	n/a	n/a
21	MYC	chr2:40007940-40009019	NB4	blood:	n/a	n/a
22	MAFF	chr2:40008131-40008541	K562	blood:	n/a	n/a
23	RUNX3	chr2:40007969-40008454	GM12878	blood:	n/a	n/a
24	TBP	chr2:40007772-40008715	K562	blood:	n/a	n/a
25	IRF1	chr2:40007844-40008967	K562	blood:	n/a	chr2:40008625-40008638 chr2:40008625-40008636 chr2:40008625-40008638 chr2:40008624-40008638 chr2:40008620-40008637 chr2:40008626-40008640 chr2:40008623-40008637 chr2:40008625-40008638 chr2:40008625-40008639 chr2:40008624-40008637 chr2:40008623-40008637 chr2:40008312-40008322 chr2:40008624-40008634 chr2:40008624-40008635
26	CUX1	chr2:40008128-40008789	K562	blood:	n/a	n/a
27	CCNT2	chr2:40007710-40008576	K562	blood:	n/a	n/a
28	ZNF384	chr2:40008174-40008498	K562	blood:	n/a	n/a
29	UBTF	chr2:40007885-40008705	K562	blood:	n/a	n/a
30	GTF2B	chr2:40007881-40008450	K562	blood:	n/a	n/a
31	CBX3	chr2:40007750-40008704	K562	blood:	n/a	n/a
32	MAFF	chr2:40008038-40008677	HepG2	liver:	n/a	n/a
33	IRF1	chr2:40007805-40008968	K562	blood:	n/a	chr2:40008625-40008638 chr2:40008625-40008636 chr2:40008625-40008638 chr2:40008624-40008638 chr2:40008620-40008637 chr2:40008626-40008640 chr2:40008623-40008637 chr2:40008625-40008638 chr2:40008625-40008639 chr2:40008624-40008637 chr2:40008623-40008637 chr2:40008312-40008322 chr2:40008624-40008634 chr2:40008624-40008635
34	MAFK	chr2:40007868-40008555	HepG2	liver:	n/a	chr2:40008378-40008394
35	MAX	chr2:40007905-40008656	K562	blood:	n/a	n/a
36	TBL1XR1	chr2:40008109-40008457	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40004284..40008257-chr2:40008263..40012278,6	MCF-7	breast:

Variant related genes	Relation type
THUMPD2	TF binding region
ENSG00000138050	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17024328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs59757140	0.96[ASN][1000 genomes]
rs6544240	0.81[ASN][1000 genomes]
rs7570829	0.80[ASN][1000 genomes]
rs7576551	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40004200-40008800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:40005600-40008600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr2:40006600-40008600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:40006600-40008800	Flanking Active TSS	K562	blood
5	chr2:40006600-40010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:40006800-40008600	Enhancers	Primary T cells from cord blood	blood
7	chr2:40006800-40008800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr2:40006800-40008800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:40006800-40010200	Weak transcription	Esophagus	oesophagus
10	chr2:40006800-40014000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:40007000-40008600	Enhancers	Primary B cells from peripheral blood	blood
12	chr2:40007000-40008600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:40007000-40008600	Enhancers	Brain Substantia Nigra	brain
14	chr2:40007000-40008600	Enhancers	GM12878-XiMat	blood
15	chr2:40007000-40010000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:40007000-40010000	Weak transcription	NHEK	skin
17	chr2:40007000-40010200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:40007000-40010200	Weak transcription	Placenta	Placenta
19	chr2:40007000-40010400	Weak transcription	NH-A	brain
20	chr2:40007200-40009400	Weak transcription	Brain Angular Gyrus	brain
21	chr2:40007200-40010000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:40007600-40008600	Enhancers	Dnd41	blood
23	chr2:40007800-40008600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:40007800-40008600	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr2:40007800-40008600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr2:40007800-40008600	Enhancers	NHLF	lung
27	chr2:40007800-40008800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:40007800-40009000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr2:40007800-40010600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:40008000-40008600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:40008000-40008600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr2:40008000-40008600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:40008000-40008600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr2:40008000-40008600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr2:40008000-40008600	Enhancers	Brain Hippocampus Middle	brain
36	chr2:40008000-40008600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:40008000-40008600	Enhancers	Colonic Mucosa	Colon
38	chr2:40008000-40008600	Flanking Active TSS	Fetal Thymus	thymus
39	chr2:40008000-40008600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr2:40008000-40008600	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr2:40008000-40008600	Enhancers	Right Atrium	heart
42	chr2:40008000-40008600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr2:40008000-40008600	Flanking Bivalent TSS/Enh	HepG2	liver
44	chr2:40008000-40008800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:40008000-40008800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr2:40008000-40008800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr2:40008000-40008800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:40008000-40009200	Enhancers	Fetal Muscle Leg	muscle
49	chr2:40008000-40010000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:40008000-40010600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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