Variant report

Variant	rs13317610
Chromosome Location	chr3:98618761-98618762
allele	C/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	POLR2A	chr3:98618321-98620638	SK-N-SH	brain:	n/a	n/a
2	SIN3AK20	chr3:98618761-98619174	A549	lung:	n/a	n/a
3	MYC	chr3:98618500-98619417	MCF10A-Er-Src	breast:	n/a	n/a
4	BCL3	chr3:98618365-98619205	A549	lung:	n/a	n/a
5	FOS	chr3:98618578-98618824	MCF10A-Er-Src	breast:	n/a	n/a
6	MAX	chr3:98618295-98619513	A549	lung:	n/a	n/a
7	POLR2A	chr3:98618470-98618805	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:98618257-98622361	U87	brain:	n/a	n/a
9	POLR2A	chr3:98618207-98618796	HCT-116	colon:	n/a	n/a
10	POLR2A	chr3:98618299-98622361	U87	brain:	n/a	n/a
11	POLR2A	chr3:98618341-98621471	ProgFib	skin:	n/a	n/a
12	POLR2A	chr3:98618148-98622423	U87	brain:	n/a	n/a
13	REST	chr3:98618368-98619272	A549	lung:	n/a	n/a
14	TAF1	chr3:98617981-98618799	A549	lung:	n/a	n/a
15	SIN3AK20	chr3:98618345-98619139	A549	lung:	n/a	n/a
16	RCOR1	chr3:98618712-98618775	K562	blood:	n/a	n/a
17	POLR2A	chr3:98618120-98622417	U87	brain:	n/a	n/a
18	POLR2A	chr3:98618477-98619014	A549	lung:	n/a	n/a
19	CHD1	chr3:98618292-98622396	IMR90	lung:	n/a	chr3:98620361-98620371
20	TCF12	chr3:98618229-98622320	A549	lung:	n/a	n/a
21	POLR2A	chr3:98615281-98622405	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000239462	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10084679	0.88[ASN][1000 genomes]
rs12330381	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13318960	0.85[AMR][1000 genomes]
rs13320266	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320890	0.85[EUR][1000 genomes]
rs13322253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327449	0.88[EUR][1000 genomes]
rs13327485	0.88[EUR][1000 genomes]
rs28417568	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28429424	0.82[ASN][1000 genomes]
rs28489284	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28528154	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28650813	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28821579	0.94[EUR][1000 genomes]
rs28883308	0.88[EUR][1000 genomes]
rs3796133	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56172805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56857413	0.94[ASN][1000 genomes]
rs57962467	0.94[ASN][1000 genomes]
rs59906228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72932691	0.82[ASN][1000 genomes]
rs72932700	0.83[ASN][1000 genomes]
rs72934623	0.88[ASN][1000 genomes]
rs72934641	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs72938540	0.86[EUR][1000 genomes]
rs72938577	0.94[ASN][1000 genomes]
rs9289696	0.86[EUR][1000 genomes]
rs9289699	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9289700	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9810407	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812438	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9818215	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819279	0.86[EUR][1000 genomes]
rs9819309	0.94[EUR][1000 genomes]
rs9828045	0.94[EUR][1000 genomes]
rs9833945	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836915	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838166	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838238	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838706	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9842226	0.86[EUR][1000 genomes]
rs9848335	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9848583	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850469	0.86[EUR][1000 genomes]
rs9852889	0.86[EUR][1000 genomes]
rs9859042	0.86[EUR][1000 genomes]
rs9862660	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9864010	0.86[EUR][1000 genomes]
rs9870500	0.82[ASN][1000 genomes]
rs9870940	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9872073	0.85[EUR][1000 genomes]
rs9872301	0.88[EUR][1000 genomes]
rs9879302	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9883751	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
2	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:98611400-98618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:98611400-98619200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:98612000-98618800	Weak transcription	Psoas Muscle	Psoas
6	chr3:98613200-98618800	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:98613200-98619200	Weak transcription	Aorta	Aorta
8	chr3:98613200-98619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:98613600-98619400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:98614200-98619600	Weak transcription	Gastric	stomach
11	chr3:98614400-98619000	Weak transcription	K562	blood
12	chr3:98615000-98619400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:98615000-98620400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:98615600-98619600	Flanking Active TSS	HUVEC	blood vessel
15	chr3:98615600-98621200	Active TSS	NHLF	lung
16	chr3:98616600-98618800	Active TSS	Muscle Satellite Cultured Cells	--
17	chr3:98616600-98621400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:98616800-98621200	Active TSS	NHDF-Ad	bronchial
19	chr3:98617400-98621200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:98617400-98622000	Active TSS	Right Ventricle	heart
21	chr3:98617600-98621200	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr3:98618000-98619000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:98618200-98618800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:98618200-98618800	Enhancers	Fetal Lung	lung
25	chr3:98618200-98619000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:98618200-98619000	Enhancers	Rectal Smooth Muscle	rectum
27	chr3:98618200-98619400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:98618200-98619400	Enhancers	Fetal Brain Male	brain
29	chr3:98618200-98619600	Transcr. at gene 5' and 3'	Osteobl	bone
30	chr3:98618200-98621800	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr3:98618400-98618800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:98618400-98618800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:98618400-98618800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:98618400-98618800	Flanking Active TSS	Fetal Heart	heart
35	chr3:98618400-98618800	Enhancers	Hela-S3	cervix
36	chr3:98618400-98619000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:98618400-98619000	Enhancers	Brain Anterior Caudate	brain
38	chr3:98618400-98619000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:98618400-98619000	Transcr. at gene 5' and 3'	HSMM	muscle
40	chr3:98618400-98619200	Enhancers	Colon Smooth Muscle	Colon
41	chr3:98618400-98619200	Flanking Active TSS	HepG2	liver
42	chr3:98618400-98619400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr3:98618400-98619400	Transcr. at gene 5' and 3'	A549	lung
44	chr3:98618400-98619600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:98618400-98619600	Transcr. at gene 5' and 3'	NH-A	brain
46	chr3:98618400-98619600	Transcr. at gene 5' and 3'	NHEK	skin
47	chr3:98618400-98619800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:98618400-98619800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr3:98618400-98619800	Active TSS	Brain Germinal Matrix	brain
50	chr3:98618400-98619800	Flanking Active TSS	Fetal Brain Female	brain

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