Variant report

Variant	rs9843677
Chromosome Location	chr3:49841962-49841963
allele	A/G
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	CTCF	chr3:49841840-49841990	GM12868	blood:	n/a	n/a
2	POLR2A	chr3:49839994-49842429	GM12878	blood:	n/a	n/a
3	PML	chr3:49839876-49842004	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:49840564-49844844	GM12892	blood:	n/a	n/a
5	MXI1	chr3:49839819-49843464	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:49839914-49845521	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:49841817-49842631	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:49840600-49844841	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:49840052-49844784	HL-60	blood:	n/a	n/a
10	ZNF263	chr3:49841375-49842096	HEK293-T-REx	kidney:	n/a	chr3:49841750-49841771
11	MXI1	chr3:49839879-49842062	IMR90	lung:	n/a	n/a
12	MAX	chr3:49841752-49842011	K562	blood:	n/a	n/a
13	MYC	chr3:49840010-49842035	NB4	blood:	n/a	chr3:49841117-49841127
14	POLR2A	chr3:49841624-49842221	K562	blood:	n/a	n/a
15	POLR2A	chr3:49840031-49844843	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:49840221-49842254	GM19193	blood:	n/a	n/a
17	POLR2A	chr3:49840589-49844877	GM12892	blood:	n/a	n/a
18	MTA3	chr3:49839849-49845759	GM12878	blood:	n/a	n/a
19	ELF1	chr3:49839946-49842453	GM12878	blood:	n/a	chr3:49840675-49840684 chr3:49840678-49840687 chr3:49840676-49840688 chr3:49840679-49840691 chr3:49841330-49841341
20	POLR2A	chr3:49841641-49842011	K562	blood:	n/a	n/a
21	POLR2A	chr3:49839942-49845851	GM12892	blood:	n/a	n/a
22	POLR2A	chr3:49840584-49842268	HL-60	blood:	n/a	n/a
23	MAX	chr3:49839978-49842023	NB4	blood:	n/a	chr3:49841117-49841127
24	POLR2A	chr3:49839998-49842558	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49839049..49842350-chr3:49936029..49940414,4	K562	blood:
2	chr3:49840341..49842910-chr3:49967049..49969753,2	K562	blood:
3	chr3:49840382..49843169-chr3:49936309..49938239,3	K562	blood:
4	chr3:49841336..49843008-chr3:49843485..49845205,2	MCF-7	breast:

Variant related genes	Relation type
CDHR4	TF binding region
ENSG00000263506	Chromatin interaction
ENSG00000230698	Chromatin interaction
ENSG00000182179	Chromatin interaction
ENSG00000164077	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13326722	1.00[ASW][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs17050876	0.82[AFR][1000 genomes]
rs4688759	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs9822349	1.00[AMR][1000 genomes]
rs9853352	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs9854341	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9858428	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs9990421	1.00[AMR][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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong 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 lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49840000-49842400	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr3:49840200-49842000	Active TSS	Fetal Kidney	kidney
3	chr3:49840800-49842000	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr3:49840800-49842400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
5	chr3:49840800-49843600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr3:49840800-49843600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr3:49841000-49842000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:49841000-49842000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:49841000-49842000	Flanking Active TSS	Brain Hippocampus Middle	brain
10	chr3:49841000-49842000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
11	chr3:49841000-49842400	Flanking Active TSS	Placenta	Placenta
12	chr3:49841000-49843600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:49841000-49845000	Enhancers	Liver	Liver
14	chr3:49841200-49842000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:49841200-49842000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:49841200-49842000	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr3:49841200-49842000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:49841200-49842000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr3:49841200-49842000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr3:49841200-49842000	Flanking Active TSS	Right Ventricle	heart
21	chr3:49841200-49842000	Flanking Active TSS	GM12878-XiMat	blood
22	chr3:49841200-49842200	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr3:49841200-49842200	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr3:49841200-49842600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:49841200-49843400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr3:49841200-49843600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr3:49841200-49843600	Flanking Active TSS	HUVEC	blood vessel
28	chr3:49841400-49842000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:49841400-49842000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:49841400-49842000	Transcr. at gene 5' and 3'	NHLF	lung
31	chr3:49841400-49842200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:49841400-49842200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr3:49841400-49842200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:49841400-49842200	Flanking Active TSS	Lung	lung
35	chr3:49841400-49842400	Flanking Active TSS	HMEC	breast
36	chr3:49841400-49842600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
37	chr3:49841400-49842800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:49841400-49844200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
39	chr3:49841400-49845200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:49841400-49845800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
41	chr3:49841400-49845800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:49841400-49846400	Weak transcription	Ovary	ovary
43	chr3:49841400-49847000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr3:49841600-49842000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:49841600-49842000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr3:49841600-49842000	Enhancers	Brain Substantia Nigra	brain
47	chr3:49841600-49842000	Flanking Active TSS	Fetal Lung	lung
48	chr3:49841600-49842200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:49841600-49842200	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr3:49841600-49842200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon

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