Variant report

Variant	rs56322058
Chromosome Location	chr3:98619289-98619290
allele	A/C
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	MAZ	chr3:98619241-98621681	IMR90	lung:	n/a	n/a
3	MYC	chr3:98618500-98619417	MCF10A-Er-Src	breast:	n/a	n/a
4	TAF1	chr3:98619078-98621229	A549	lung:	n/a	n/a
5	POLR2A	chr3:98619004-98619308	MCF10A-Er-Src	breast:	n/a	n/a
6	SP1	chr3:98619263-98621521	HCT-116	colon:	n/a	chr3:98620772-98620783 chr3:98620982-98620996 chr3:98621186-98621196 chr3:98620576-98620588 chr3:98620772-98620784 chr3:98621186-98621195 chr3:98620577-98620587 chr3:98621182-98621196 chr3:98620576-98620588 chr3:98620773-98620787 chr3:98620392-98620401 chr3:98620772-98620784 chr3:98620577-98620587
7	MAX	chr3:98618295-98619513	A549	lung:	n/a	n/a
8	POLR2A	chr3:98618257-98622361	U87	brain:	n/a	n/a
9	POLR2A	chr3:98619057-98621173	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:98619206-98621801	HCT-116	colon:	n/a	n/a
11	POLR2A	chr3:98618299-98622361	U87	brain:	n/a	n/a
12	POLR2A	chr3:98618341-98621471	ProgFib	skin:	n/a	n/a
13	POLR2A	chr3:98618148-98622423	U87	brain:	n/a	n/a
14	POLR2A	chr3:98618120-98622417	U87	brain:	n/a	n/a
15	CHD1	chr3:98618292-98622396	IMR90	lung:	n/a	chr3:98620361-98620371
16	MXI1	chr3:98618881-98621804	IMR90	lung:	n/a	n/a
17	TCF12	chr3:98618229-98622320	A549	lung:	n/a	n/a
18	POLR2A	chr3:98615281-98622405	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
ENSG00000239462	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10433438	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511169	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511171	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935518	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935542	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935564	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708475	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716000	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716007	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716281	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716579	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719660	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914591	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914715	0.89[EUR][1000 genomes]
rs11916285	0.92[EUR][1000 genomes]
rs11918243	0.97[ASN][1000 genomes]
rs11918944	0.91[ASN][1000 genomes]
rs11920205	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11920327	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11922078	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923486	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923805	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11928233	0.91[ASN][1000 genomes]
rs12203	0.89[EUR][1000 genomes]
rs13069458	0.91[ASN][1000 genomes]
rs1440154	0.92[EUR][1000 genomes]
rs1471588	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16840260	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846347	0.88[EUR][1000 genomes]
rs17210963	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17212369	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17213336	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17278047	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278278	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17852693	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822017	0.89[EUR][1000 genomes]
rs1827158	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278599	0.89[EUR][1000 genomes]
rs3772100	0.90[EUR][1000 genomes]
rs55650073	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55662129	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55730510	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55764252	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55988144	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075614	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56290036	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276861	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276862	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276864	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276869	0.91[ASN][1000 genomes]
rs62276879	0.85[ASN][1000 genomes]
rs62276883	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276884	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276885	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276888	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276909	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440159	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6440253	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66517942	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6805605	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136038	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73136045	0.89[EUR][1000 genomes]
rs73136048	0.89[EUR][1000 genomes]
rs73136057	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73136060	0.87[EUR][1000 genomes]
rs73138004	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73138027	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138030	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138048	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138053	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138055	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138058	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73138063	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138082	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140009	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140027	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140032	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7432439	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7614892	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629550	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638009	0.91[ASN][1000 genomes]
rs7642785	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644946	0.92[EUR][1000 genomes]
rs8179927	0.92[EUR][1000 genomes]
rs982291	0.91[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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
2	chr3:98613200-98619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:98613600-98619400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:98614200-98619600	Weak transcription	Gastric	stomach
5	chr3:98615000-98619400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:98615000-98620400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:98615600-98619600	Flanking Active TSS	HUVEC	blood vessel
8	chr3:98615600-98621200	Active TSS	NHLF	lung
9	chr3:98616600-98621400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:98616800-98621200	Active TSS	NHDF-Ad	bronchial
11	chr3:98617400-98621200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:98617400-98622000	Active TSS	Right Ventricle	heart
13	chr3:98617600-98621200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr3:98618200-98619400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:98618200-98619400	Enhancers	Fetal Brain Male	brain
16	chr3:98618200-98619600	Transcr. at gene 5' and 3'	Osteobl	bone
17	chr3:98618200-98621800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr3:98618400-98619400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr3:98618400-98619400	Transcr. at gene 5' and 3'	A549	lung
20	chr3:98618400-98619600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:98618400-98619600	Transcr. at gene 5' and 3'	NH-A	brain
22	chr3:98618400-98619600	Transcr. at gene 5' and 3'	NHEK	skin
23	chr3:98618400-98619800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:98618400-98619800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr3:98618400-98619800	Active TSS	Brain Germinal Matrix	brain
26	chr3:98618400-98619800	Flanking Active TSS	Fetal Brain Female	brain
27	chr3:98618400-98621200	Active TSS	H1 Cell Line	embryonic stem cell
28	chr3:98618400-98621200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr3:98618400-98621200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:98618400-98621200	Active TSS	Fetal Kidney	kidney
31	chr3:98618400-98621200	Active TSS	GM12878-XiMat	blood
32	chr3:98618400-98621400	Active TSS	Left Ventricle	heart
33	chr3:98618400-98621600	Active TSS	Right Atrium	heart
34	chr3:98618400-98621800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:98618600-98619400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:98618600-98619400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:98618600-98619400	Active TSS	Fetal Muscle Leg	muscle
38	chr3:98618600-98619600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:98618600-98619600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:98618600-98619600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:98618600-98619600	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:98618600-98619800	Flanking Active TSS	Dnd41	blood
43	chr3:98618600-98620000	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr3:98618600-98621200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:98618600-98621400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:98618600-98621600	Active TSS	Ovary	ovary
47	chr3:98618600-98621800	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr3:98618600-98621800	Active TSS	HSMMtube	muscle
49	chr3:98618800-98619400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:98618800-98619400	Flanking Active TSS	Fetal Lung	lung

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