Variant report

Variant	rs373162085
Chromosome Location	chr3:23986199-23986200
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	MAX	chr3:23986061-23988244	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
2	ELK1	chr3:23985919-23986218	K562	blood:	n/a	n/a
3	MYC	chr3:23985630-23988292	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23985779-23985795 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
4	POLR2A	chr3:23986095-23988262	H1-neurons	neurons:	n/a	n/a
5	USF2	chr3:23986143-23986246	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:23986104-23988409	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr3:23986183-23986754	A549	lung:	n/a	chr3:23986483-23986490 chr3:23986479-23986491 chr3:23986483-23986490 chr3:23986483-23986490
8	MAZ	chr3:23985991-23988385	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
9	POLR2A	chr3:23986132-23988235	K562	blood:	n/a	n/a
10	REST	chr3:23985970-23988483	H1-neurons	neurons:	n/a	chr3:23988106-23988119 chr3:23986726-23986739 chr3:23988103-23988116
11	ZBTB7A	chr3:23986178-23986704	ECC-1	luminal epithelium:	n/a	n/a
12	TBP	chr3:23986094-23988447	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAZ	chr3:23986016-23989986	IMR90	lung:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
14	MYC	chr3:23985627-23988307	K562	blood:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23985779-23985795 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
15	POLR2A	chr3:23985541-23990663	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr3:23985307-23988519	SK-N-SH	brain:	n/a	chr3:23987345-23987354
17	CHD2	chr3:23986130-23986942	GM12878	blood:	n/a	n/a
18	HCFC1	chr3:23986135-23986232	K562	blood:	n/a	n/a
19	HCFC1	chr3:23985923-23988484	Hela-S3	cervix:	n/a	n/a
20	JUND	chr3:23986133-23986903	H1-hESC	embryonic stem cell:	n/a	chr3:23986448-23986457
21	POLR2A	chr3:23985896-23986227	HepG2	liver:	n/a	n/a
22	TAF1	chr3:23986178-23988204	H1-hESC	embryonic stem cell:	n/a	n/a
23	RCOR1	chr3:23985950-23986922	K562	blood:	n/a	n/a
24	MAX	chr3:23986188-23988424	A549	lung:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
25	TCF7L2	chr3:23985939-23986226	HEK293	kidney:	n/a	n/a
26	CHD2	chr3:23986109-23986838	H1-hESC	embryonic stem cell:	n/a	n/a
27	BHLHE40	chr3:23985728-23988393	K562	blood:	n/a	chr3:23986706-23986722 chr3:23986783-23986799 chr3:23987153-23987169 chr3:23987430-23987446 chr3:23987438-23987454 chr3:23987441-23987457 chr3:23987189-23987205
28	RCOR1	chr3:23985939-23986993	K562	blood:	n/a	n/a
29	TCF7L2	chr3:23985975-23986216	PANC-1	pancreas:	n/a	n/a
30	MXI1	chr3:23985536-23988397	IMR90	lung:	n/a	chr3:23987345-23987354
31	TBP	chr3:23986109-23988318	K562	blood:	n/a	n/a
32	ZNF384	chr3:23986073-23986215	K562	blood:	n/a	n/a
33	SIN3A	chr3:23985912-23988449	H1-hESC	embryonic stem cell:	n/a	chr3:23987199-23987210 chr3:23987852-23987863 chr3:23986774-23986785 chr3:23986898-23986909

No.	Distal block	Cell Line	Cell type
1	chr15:78422464..78425441-chr3:23985742..23987944,2	MCF-7	breast:
2	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
3	chr3:23986158..23988420-chr3:24004373..24006448,3	MCF-7	breast:
4	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
5	chr3:23985869..23987641-chr3:24536460..24539004,2	MCF-7	breast:
6	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
NR1D2	TF binding region
ENSG00000151090	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000166411	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000136425	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv3449153	chr3:23984948-23988646	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3406325	chr3:23985473-23988321	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	esv3425301	chr3:23985548-23988496	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23985200-23986200	Flanking Active TSS	Fetal Heart	heart
2	chr3:23985200-23986200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr3:23985400-23986200	Enhancers	Primary B cells from peripheral blood	blood
4	chr3:23985400-23986600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr3:23985600-23986200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:23985600-23986200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:23985600-23986200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr3:23985600-23986200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr3:23985600-23986200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr3:23985600-23986200	Flanking Active TSS	K562	blood
11	chr3:23985600-23986400	Bivalent/Poised TSS	Thymus	Thymus
12	chr3:23985600-23986600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:23985600-23988200	Active TSS	Fetal Kidney	kidney
14	chr3:23985600-23988400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:23985600-23988800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr3:23985800-23986200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:23985800-23986200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:23985800-23986200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:23985800-23986200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:23985800-23986200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:23985800-23986200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:23985800-23986200	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr3:23985800-23986200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr3:23985800-23986200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr3:23985800-23986200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:23985800-23986200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr3:23985800-23986200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:23985800-23986200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr3:23985800-23986200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:23985800-23986200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:23985800-23986200	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr3:23985800-23986200	Flanking Active TSS	Liver	Liver
33	chr3:23985800-23986200	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr3:23985800-23986200	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr3:23985800-23986200	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr3:23985800-23986200	Flanking Active TSS	Fetal Brain Male	brain
37	chr3:23985800-23986200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr3:23985800-23986200	Flanking Active TSS	Fetal Lung	lung
39	chr3:23985800-23986200	Flanking Active TSS	Fetal Stomach	stomach
40	chr3:23985800-23986200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr3:23985800-23986200	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr3:23985800-23986200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr3:23985800-23986200	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr3:23985800-23986200	Flanking Active TSS	GM12878-XiMat	blood
45	chr3:23985800-23986200	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
46	chr3:23985800-23986200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
47	chr3:23985800-23986200	Flanking Active TSS	NHDF-Ad	bronchial
48	chr3:23985800-23986200	Flanking Active TSS	NHLF	lung
49	chr3:23985800-23986600	Active TSS	Primary T cells from cord blood	blood
50	chr3:23985800-23987600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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