Variant report

Variant	rs9876937
Chromosome Location	chr3:42642697-42642698
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:277)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:277 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr3:42642590-42642951	MCF10A-Er-Src	breast:	n/a	n/a
2	BHLHE40	chr3:42641481-42642847	K562	blood:	n/a	n/a
3	TAF1	chr3:42641582-42642991	H1-neurons	neurons:	n/a	n/a
4	YY1	chr3:42641655-42642888	K562	blood:	n/a	n/a
5	GABPA	chr3:42642469-42642903	K562	blood:	n/a	n/a
6	MAX	chr3:42641527-42642990	Hela-S3	cervix:	n/a	n/a
7	MYC	chr3:42641642-42642837	K562	blood:	n/a	n/a
8	ZBTB7A	chr3:42641850-42642872	K562	blood:	n/a	n/a
9	TAF1	chr3:42641523-42643011	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr3:42641595-42642858	A549	lung:	n/a	n/a
11	HEY1	chr3:42641533-42642927	K562	blood:	n/a	n/a
12	ZNF143	chr3:42641630-42643068	Hela-S3	cervix:	n/a	n/a
13	SIN3A	chr3:42641367-42643156	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:42641539-42642959	GM15510	blood:	n/a	n/a
15	GTF2B	chr3:42641678-42642852	K562	blood:	n/a	n/a
16	CTCF	chr3:42642660-42642810	GM12875	blood:	n/a	n/a
17	POLR2A	chr3:42641414-42642833	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:42641593-42644059	K562	blood:	n/a	n/a
19	POLR2A	chr3:42641498-42642793	ECC-1	luminal epithelium:	n/a	n/a
20	SMC3	chr3:42641487-42642965	Hela-S3	cervix:	n/a	n/a
21	TAF1	chr3:42641553-42642910	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:42642564-42642945	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:42641403-42642884	HUVEC	blood vessel:	n/a	n/a
24	E2F6	chr3:42641621-42642947	K562	blood:	n/a	chr3:42642320-42642332 chr3:42641918-42641927 chr3:42642321-42642332
25	PML	chr3:42641354-42643034	K562	blood:	n/a	n/a
26	POLR2A	chr3:42641617-42642752	HepG2	liver:	n/a	n/a
27	YY1	chr3:42641763-42642762	GM12892	blood:	n/a	n/a
28	CTCF	chr3:42642646-42642986	K562	blood:	n/a	n/a
29	POLR2A	chr3:42641469-42643076	GM12892	blood:	n/a	n/a
30	MAZ	chr3:42641479-42643050	K562	blood:	n/a	n/a
31	CHD1	chr3:42642636-42643554	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:42641528-42642918	Raji	blood:	n/a	n/a
33	CTCF	chr3:42642660-42642810	GM12865	blood:	n/a	n/a
34	SIN3AK20	chr3:42641547-42642936	SK-N-SH	brain:	n/a	n/a
35	MXI1	chr3:42641601-42643080	K562	blood:	n/a	n/a
36	GABPA	chr3:42642566-42642986	K562	blood:	n/a	n/a
37	POLR2A	chr3:42641525-42642987	H1-neurons	neurons:	n/a	n/a
38	ZKSCAN1	chr3:42641637-42642911	Hela-S3	cervix:	n/a	n/a
39	ZNF384	chr3:42641054-42643109	K562	blood:	n/a	n/a
40	HA-E2F1	chr3:42642580-42643055	MCF-7	breast:	n/a	n/a
41	POLR2A	chr3:42641554-42642950	GM18951	blood:	n/a	n/a
42	ZBTB7A	chr3:42641812-42642875	K562	blood:	n/a	n/a
43	POLR2A	chr3:42641463-42642963	HL-60	blood:	n/a	n/a
44	POLR2A	chr3:42641398-42643075	Hela-S3	cervix:	n/a	n/a
45	TBP	chr3:42641275-42643032	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr3:42641443-42642890	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:42641571-42642897	NB4	blood:	n/a	n/a
48	EBF1	chr3:42642349-42642912	GM12878	blood:	n/a	chr3:42642683-42642694
49	TEAD4	chr3:42641408-42644046	K562	blood:	n/a	n/a
50	POLR2A	chr3:42641510-42642972	GM18505	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:120840217..120840878-chr3:42642130..42642750,2	Hela-S3	cervix:
2	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
3	chr3:42640361..42643591-chr3:42693270..42696162,5	K562	blood:
4	chr3:42509273..42511295-chr3:42641295..42643446,2	MCF-7	breast:
5	chr3:42604560..42606277-chr3:42641170..42643967,2	K562	blood:
6	chr3:42640678..42643591-chr3:42694568..42696079,2	K562	blood:
7	chr3:42621283..42625330-chr3:42639303..42643596,7	MCF-7	breast:
8	chr3:42604086..42606277-chr3:42642467..42644274,2	K562	blood:
9	chr3:42639395..42643636-chr3:42699754..42702498,4	K562	blood:
10	chr2:10829919..10830572-chr3:42642142..42643049,2	Hela-S3	cervix:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SS18L2-2	chr3:42642476-42644548	NONHSAT089241

No data

Variant related genes	Relation type
SEC22C	TF binding region
ENSG00000008324	Chromatin interaction
ENSG00000115761	Chromatin interaction
ENSG00000107581	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000235787	Chromatin interaction
ENSG00000243819	Chromatin interaction
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10154957	1.00[AMR][1000 genomes]
rs13320598	1.00[AMR][1000 genomes]
rs13320629	1.00[YRI][hapmap]
rs13325536	1.00[AMR][1000 genomes]
rs28508060	1.00[AMR][1000 genomes]
rs28549046	1.00[AMR][1000 genomes]
rs580447	1.00[AMR][1000 genomes]
rs58273990	1.00[AMR][1000 genomes]
rs9311325	1.00[YRI][hapmap]
rs9812538	1.00[AMR][1000 genomes]
rs9812673	1.00[AMR][1000 genomes]
rs9822273	1.00[AMR][1000 genomes]
rs9832720	1.00[AMR][1000 genomes]
rs9841926	1.00[AMR][1000 genomes]
rs9844154	1.00[YRI][hapmap]
rs9847303	1.00[YRI][hapmap]
rs9849556	1.00[YRI][hapmap]
rs9853946	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9855071	1.00[AMR][1000 genomes]
rs9869491	1.00[AMR][1000 genomes]
rs9884030	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs9985232	1.00[ASW][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3404290	chr3:42638948-42643146	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42640800-42643600	Active TSS	Hela-S3	cervix
2	chr3:42640800-42643800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:42641000-42643400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr3:42641000-42643600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:42641200-42642800	Active TSS	Brain Hippocampus Middle	brain
6	chr3:42641200-42642800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr3:42641200-42642800	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr3:42641200-42643000	Active TSS	Liver	Liver
9	chr3:42641200-42643000	Active TSS	Brain Angular Gyrus	brain
10	chr3:42641200-42643000	Active TSS	Brain Substantia Nigra	brain
11	chr3:42641200-42643000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr3:42641200-42643000	Active TSS	Stomach Smooth Muscle	stomach
13	chr3:42641200-42643000	Active TSS	NHEK	skin
14	chr3:42641200-42643000	Active TSS	Osteobl	bone
15	chr3:42641200-42643200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:42641200-42643200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:42641200-42643200	Active TSS	Fetal Lung	lung
18	chr3:42641200-42643200	Active TSS	Placenta	Placenta
19	chr3:42641200-42643400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:42641200-42643400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:42641200-42643400	Active TSS	Muscle Satellite Cultured Cells	--
22	chr3:42641200-42643400	Active TSS	Fetal Brain Female	brain
23	chr3:42641200-42643400	Active TSS	Fetal Kidney	kidney
24	chr3:42641200-42643400	Active TSS	Fetal Muscle Leg	muscle
25	chr3:42641200-42643400	Active TSS	Fetal Stomach	stomach
26	chr3:42641200-42643400	Active TSS	Fetal Thymus	thymus
27	chr3:42641200-42643400	Active TSS	Placenta Amnion	Placenta Amnion
28	chr3:42641200-42643600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:42641200-42643600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr3:42641200-42643600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:42641200-42643600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:42641200-42643600	Active TSS	Fetal Intestine Large	intestine
33	chr3:42641200-42643600	Active TSS	Fetal Muscle Trunk	muscle
34	chr3:42641200-42643600	Active TSS	K562	blood
35	chr3:42641200-42643800	Active TSS	H1 Cell Line	embryonic stem cell
36	chr3:42641200-42643800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:42641200-42643800	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr3:42641200-42643800	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr3:42641200-42643800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:42641200-42643800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:42641200-42643800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:42641200-42643800	Active TSS	Fetal Intestine Small	intestine
43	chr3:42641200-42643800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr3:42641200-42643800	Active TSS	A549	lung
45	chr3:42641200-42643800	Active TSS	HSMMtube	muscle
46	chr3:42641200-42643800	Active TSS	NHLF	lung
47	chr3:42641200-42644000	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr3:42641200-42644000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:42641200-42644000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:42641200-42644200	Active TSS	HUES48 Cell Line	embryonic stem cell

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