Variant report

Variant	rs56322743
Chromosome Location	chr1:247496080-247496081
allele	A/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	UBTF	chr1:247494404-247496504	K562	blood:	n/a	n/a
2	SIN3A	chr1:247493833-247497073	H1-hESC	embryonic stem cell:	n/a	chr1:247495631-247495642 chr1:247495953-247495964
3	MAX	chr1:247494908-247496081	MCF-7	breast:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
4	HEY1	chr1:247494289-247497747	K562	blood:	n/a	chr1:247494564-247494579
5	UBTF	chr1:247494251-247496736	K562	blood:	n/a	n/a
6	ELF1	chr1:247494100-247496415	GM12878	blood:	n/a	chr1:247495199-247495212 chr1:247494665-247494677 chr1:247496347-247496358
7	CBX3	chr1:247495003-247497040	K562	blood:	n/a	n/a
8	ZBTB7A	chr1:247494951-247496133	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr1:247495435-247496082	MCF-7	breast:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247495807-247495816
10	WRNIP1	chr1:247495720-247496224	GM12878	blood:	n/a	n/a
11	CHD1	chr1:247495781-247496498	H1-hESC	embryonic stem cell:	n/a	n/a
12	CUX1	chr1:247496020-247496115	K562	blood:	n/a	n/a
13	POLR2A	chr1:247494422-247505513	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr1:247494398-247496436	NB4	blood:	n/a	n/a
15	IRF1	chr1:247496077-247496168	K562	blood:	n/a	n/a
16	POLR2A	chr1:247494318-247498379	GM12878	blood:	n/a	n/a
17	MYC	chr1:247494439-247496518	NB4	blood:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
18	NR2F2	chr1:247495497-247496837	K562	blood:	n/a	n/a
19	ELK1	chr1:247495985-247496087	K562	blood:	n/a	n/a
20	TCF12	chr1:247495088-247496098	A549	lung:	n/a	chr1:247495950-247495960
21	POLR2A	chr1:247495662-247496449	K562	blood:	n/a	n/a
22	PML	chr1:247496078-247496711	K562	blood:	n/a	n/a
23	MYC	chr1:247494363-247496744	MCF10A-Er-Src	breast:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
24	RCOR1	chr1:247494257-247496645	K562	blood:	n/a	n/a
25	ZBTB7A	chr1:247495055-247496151	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr1:247494396-247499332	K562	blood:	n/a	n/a
27	MTA3	chr1:247495494-247496317	GM12878	blood:	n/a	n/a
28	TBP	chr1:247494395-247496204	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr1:247495590-247497683	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:247494225-247497338	GM12892	blood:	n/a	n/a
31	POLR2A	chr1:247494236-247499105	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr1:247494209-247500059	K562	blood:	n/a	n/a
33	POLR2A	chr1:247494255-247496434	GM18505	blood:	n/a	n/a
34	TEAD4	chr1:247495483-247496684	K562	blood:	n/a	n/a
35	TBP	chr1:247494371-247496557	K562	blood:	n/a	n/a
36	SMARCC1	chr1:247495074-247497550	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:247494516-247496155	GM12878	blood:	n/a	n/a
38	RUNX3	chr1:247495013-247496124	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:247493999-247497967	PFSK-1	brain:	n/a	n/a
40	MAX	chr1:247493985-247496466	K562	blood:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
41	NFATC1	chr1:247495575-247496301	GM12878	blood:	n/a	n/a
42	MYC	chr1:247495006-247496277	K562	blood:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247495807-247495816
43	JUN	chr1:247493352-247496206	K562	blood:	n/a	chr1:247495603-247495612 chr1:247494409-247494418 chr1:247495601-247495610 chr1:247494408-247494417 chr1:247495781-247495789 chr1:247495256-247495265 chr1:247495782-247495793 chr1:247495604-247495613
44	POLR2A	chr1:247494445-247501569	K562	blood:	n/a	n/a
45	MAX	chr1:247493794-247496726	K562	blood:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
46	SIN3AK20	chr1:247495067-247496140	MCF-7	breast:	n/a	n/a
47	MAX	chr1:247494327-247496421	HepG2	liver:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
48	PML	chr1:247495617-247496622	K562	blood:	n/a	n/a
49	MYC	chr1:247493850-247496299	K562	blood:	n/a	chr1:247495699-247495708 chr1:247495602-247495612 chr1:247495700-247495710 chr1:247495702-247495709 chr1:247495699-247495714 chr1:247495605-247495615 chr1:247495701-247495710 chr1:247494975-247494985 chr1:247495807-247495816
50	TBL1XR1	chr1:247495102-247496207	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:247496053-247496103	A549	lung:	n/a
2	chr1:247496053-247496103	BJ	skin:	n/a
3	chr1:247496053-247496103	HUVEC	blood vessel:	n/a
4	chr1:247496053-247496103	SK-N-MC	brain:	n/a
5	chr1:247496053-247496103	HPAEpiC	pulmonary alveolar:	n/a
6	chr1:247496053-247496103	HNPCEpiC	eye:	n/a
7	chr1:247496053-247496103	PFSK-1	brain:	n/a
8	chr1:247496053-247496103	NH-A	brain:	n/a
9	chr1:247496053-247496103	NHDF-neo	bronchial:	n/a
10	chr1:247496053-247496103	GM12892	blood:	n/a
11	chr1:247496053-247496103	HRE	kidney:	n/a
12	chr1:247496053-247496103	NHBE	bronchial:	n/a
13	chr1:247496053-247496103	MCF-7	breast:	n/a
14	chr1:247496053-247496103	SKMC	muscle:	n/a
15	chr1:247496053-247496103	IMR90	lung:	fetal
16	chr1:247496053-247496103	AoSMC	blood vessel:	n/a
17	chr1:247496053-247496103	HCT-116	colon:	n/a
18	chr1:247496053-247496103	ovcar-3	ovarian:	n/a
19	chr1:247496053-247496103	ProgFib	skin:	n/a
20	chr1:247496053-247496103	AG09309	skin:	n/a
21	chr1:247496053-247496103	NB4	blood:	n/a
22	chr1:247496053-247496103	LNCaP	prostate:	n/a
23	chr1:247496053-247496103	T-47D	breast:	n/a
24	chr1:247496053-247496103	NT2-D1	testis:	n/a
25	chr1:247496053-247496103	AG09319	gingival:	n/a
26	chr1:247496053-247496103	GM12891	blood:	n/a
27	chr1:247496053-247496103	RPTEC	kidney:	n/a
28	chr1:247496053-247496103	AG04449	skin:	fetal
29	chr1:247496053-247496103	GM19239	blood:	n/a
30	chr1:247496053-247496103	HRCEpiC	kidney:	n/a
31	chr1:247496053-247496103	U87	brain:	n/a
32	chr1:247496053-247496103	Hepatocyte	liver:	n/a
33	chr1:247496053-247496103	SK-N-SH_RA	brain:	n/a
34	chr1:247496053-247496103	HEEpiC	esophagus:	n/a
35	chr1:247496053-247496103	K562	blood:	n/a
36	chr1:247496053-247496103	HepG2	liver:	n/a
37	chr1:247496053-247496103	HRPEpiC	eye:	n/a
38	chr1:247496053-247496103	CMK	blood:	n/a
39	chr1:247496053-247496103	HCF	heart:	n/a
40	chr1:247496053-247496103	SK-N-SH	brain:	n/a
41	chr1:247496053-247496103	HL-60	blood:	n/a
42	chr1:247496053-247496103	HEK293	kidney:	embryo
43	chr1:247496053-247496103	HMEC	breast:	n/a
44	chr1:247496053-247496103	H1-hESC	embryonic stem cell:	embryo
45	chr1:247496053-247496103	HCM	heart:	n/a
46	chr1:247496053-247496103	MCF10A-Er-Src	breast:	n/a
47	chr1:247496053-247496103	HCPEpiC	choroid plexus:	n/a
48	chr1:247496053-247496103	AG04450	lung:	fetal
49	chr1:247496053-247496103	GM06990	blood:	n/a
50	chr1:247496053-247496103	GM12878	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:247371506..247373896-chr1:247494793..247496492,2	K562	blood:
2	chr1:247237656..247243483-chr1:247491762..247497969,8	K562	blood:
3	chr1:247371907..247375145-chr1:247492885..247497524,4	MCF-7	breast:
4	chr1:247450966..247454008-chr1:247495973..247498678,3	K562	blood:
5	chr1:247484098..247486215-chr1:247495440..247497543,2	K562	blood:
6	chr1:247093731..247095297-chr1:247494500..247497465,3	K562	blood:
7	chr1:247371861..247375582-chr1:247493463..247496360,5	MCF-7	breast:
8	chr1:247342736..247346262-chr1:247495942..247498816,3	K562	blood:
9	chr1:247371399..247373319-chr1:247494315..247496686,3	K562	blood:
10	chr1:247495187..247496810-chr1:247522265..247524064,2	K562	blood:
11	chr1:247473800..247482682-chr1:247490121..247498423,19	K562	blood:
12	chr1:247496074..247498986-chr1:247563500..247566011,2	K562	blood:
13	chr1:247069586..247071786-chr1:247495195..247496702,2	K562	blood:
14	chr1:247495232..247496940-chr1:247645349..247647027,2	K562	blood:
15	chr1:247093791..247096097-chr1:247493835..247497465,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NLRP3-1	chr1:247496030-247497728	NONHSAT010772
2	lnc-NLRP3-1	chr1:247495658-247496689	NONHSAT010773
3	lnc-NLRP3-1	chr1:247495187-247498708	NONHSAT010771

Variant related genes	Relation type
ZNF496	TF binding region
ZNF496	CpG island
ENSG00000135747	Chromatin interaction
ENSG00000153207	Chromatin interaction
ENSG00000227671	Chromatin interaction
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1057996	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732300	1.00[ASN][1000 genomes]
rs10924980	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924984	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1192835	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1192836	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239714	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846406	1.00[EUR][1000 genomes]
rs1771919	1.00[EUR][1000 genomes]
rs1771928	1.00[EUR][1000 genomes]
rs1771944	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771945	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771946	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778548	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891074	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793288	1.00[EUR][1000 genomes]
rs2799179	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501868	1.00[ASN][1000 genomes]
rs4925535	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57178323	1.00[EUR][1000 genomes]
rs61276550	1.00[EUR][1000 genomes]
rs6657577	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669714	1.00[EUR][1000 genomes]
rs6671690	1.00[EUR][1000 genomes]
rs6676056	1.00[EUR][1000 genomes]
rs6689651	1.00[EUR][1000 genomes]
rs74152973	0.91[EUR][1000 genomes]
rs74152980	1.00[EUR][1000 genomes]
rs74152988	1.00[EUR][1000 genomes]
rs74152993	1.00[EUR][1000 genomes]
rs7517006	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947174	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
3	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a
5	nsv873439	chr1:247486736-247549220	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a
6	esv3437414	chr1:247494354-247496902	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
7	esv1799864	chr1:247494789-247500650	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247493600-247496400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:247493800-247496200	Active TSS	HSMMtube	muscle
3	chr1:247493800-247496400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:247493800-247496600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:247494000-247496400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:247494000-247496400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:247494000-247496400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:247494000-247496400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:247494000-247496400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:247494000-247496400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:247494000-247496600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:247494000-247496600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:247494200-247496200	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:247494200-247496200	Active TSS	Aorta	Aorta
15	chr1:247494200-247496200	Active TSS	Brain Cingulate Gyrus	brain
16	chr1:247494200-247496200	Active TSS	Colon Smooth Muscle	Colon
17	chr1:247494200-247496200	Active TSS	A549	lung
18	chr1:247494200-247496200	Active TSS	HSMM	muscle
19	chr1:247494200-247496400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr1:247494200-247496400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:247494200-247496400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:247494200-247496400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:247494200-247496400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:247494200-247496400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:247494200-247496400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:247494200-247496400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:247494200-247496400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:247494200-247496400	Active TSS	Fetal Intestine Small	intestine
29	chr1:247494200-247496400	Active TSS	Fetal Kidney	kidney
30	chr1:247494200-247496400	Active TSS	Gastric	stomach
31	chr1:247494200-247496600	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:247494200-247496600	Active TSS	Ovary	ovary
33	chr1:247494200-247496800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:247494400-247496200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:247494400-247496200	Active TSS	Osteobl	bone
36	chr1:247494400-247496400	Active TSS	Brain Hippocampus Middle	brain
37	chr1:247494400-247496400	Active TSS	Esophagus	oesophagus
38	chr1:247494400-247496400	Active TSS	Right Atrium	heart
39	chr1:247494400-247496400	Active TSS	Right Ventricle	heart
40	chr1:247494400-247496400	Active TSS	Spleen	Spleen
41	chr1:247494600-247496200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:247494600-247496400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:247495000-247496200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:247495400-247496200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr1:247495600-247496200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
46	chr1:247495600-247496200	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr1:247495600-247496400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:247495600-247496600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:247495600-247496600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:247495600-247496600	Flanking Active TSS	Adipose Nuclei	Adipose

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