Variant report

Variant	rs559499939
Chromosome Location	chr1:247495625-247495626
allele	C/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	CTCF	chr1:247495580-247495730	SAEC	small airway:	n/a	n/a
5	TAF1	chr1:247494284-247495892	H1-hESC	embryonic stem cell:	n/a	n/a
6	HEY1	chr1:247494289-247497747	K562	blood:	n/a	chr1:247494564-247494579
7	BHLHE40	chr1:247495097-247495885	HepG2	liver:	n/a	chr1:247495605-247495621
8	POLR2A	chr1:247495520-247496079	GM12892	blood:	n/a	n/a
9	MAX	chr1:247494953-247495971	SK-N-SH	brain:	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
10	UBTF	chr1:247494251-247496736	K562	blood:	n/a	n/a
11	POLR2A	chr1:247494334-247495960	Hela-S3	cervix:	n/a	n/a
12	HEY1	chr1:247495616-247495945	K562	blood:	n/a	n/a
13	USF1	chr1:247495438-247495902	ECC-1	luminal epithelium:	n/a	chr1:247495605-247495621
14	MAX	chr1:247495061-247495909	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 chr1:247495807-247495816
15	NR2F2	chr1:247495625-247495936	K562	blood:	n/a	n/a
16	ZBTB7A	chr1:247495010-247495966	K562	blood:	n/a	n/a
17	ELF1	chr1:247494100-247496415	GM12878	blood:	n/a	chr1:247495199-247495212 chr1:247494665-247494677 chr1:247496347-247496358
18	ELF1	chr1:247494925-247495994	MCF-7	breast:	n/a	chr1:247495199-247495212
19	CBX3	chr1:247495003-247497040	K562	blood:	n/a	n/a
20	ZBTB7A	chr1:247494951-247496133	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr1:247494856-247495863	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr1:247494338-247495763	SK-N-SH	brain:	n/a	n/a
23	MYBL2	chr1:247495487-247495995	HepG2	liver:	n/a	n/a
24	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
25	POLR2A	chr1:247494337-247495995	HCT-116	colon:	n/a	n/a
26	MAX	chr1:247494376-247495977	Hela-S3	cervix:	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
27	CTCF	chr1:247495600-247495750	GM06990	blood:	n/a	n/a
28	TAF7	chr1:247494748-247495790	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr1:247495599-247495954	GM12878	blood:	n/a	n/a
30	CTCF	chr1:247495420-247495670	BJ	skin:	n/a	n/a
31	POLR2A	chr1:247494358-247495781	HEK293	kidney:	n/a	n/a
32	HDAC2	chr1:247495539-247495761	K562	blood:	n/a	n/a
33	POLR2A	chr1:247494422-247505513	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr1:247494250-247495914	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr1:247494398-247496436	NB4	blood:	n/a	n/a
36	SIN3AK20	chr1:247494785-247495832	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr1:247493944-247495972	H1-neurons	neurons:	n/a	n/a
38	MXI1	chr1:247495536-247496047	K562	blood:	n/a	n/a
39	SIN3AK20	chr1:247495575-247495793	K562	blood:	n/a	n/a
40	ELK1	chr1:247495167-247495833	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:247494318-247498379	GM12878	blood:	n/a	n/a
42	CTCF	chr1:247495600-247495750	GM12874	blood:	n/a	n/a
43	TAF1	chr1:247495549-247495908	K562	blood:	n/a	n/a
44	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
45	POLR2A	chr1:247494315-247496009	K562	blood:	n/a	n/a
46	FOXP2	chr1:247495523-247495894	PFSK-1	brain:	n/a	n/a
47	NR2F2	chr1:247495497-247496837	K562	blood:	n/a	n/a
48	POLR2A	chr1:247494925-247495635	K562	blood:	n/a	n/a
49	TCF12	chr1:247495088-247496098	A549	lung:	n/a	chr1:247495950-247495960
50	MAX	chr1:247495215-247495918	A549	lung:	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

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	chr1:247484098..247486215-chr1:247495440..247497543,2	K562	blood:
5	chr1:247495103..247495785-chr11:66056230..66056965,2	Hela-S3	cervix:
6	chr1:247093731..247095297-chr1:247494500..247497465,3	K562	blood:
7	chr1:247371861..247375582-chr1:247493463..247496360,5	MCF-7	breast:
8	chr1:247266988..247268956-chr1:247494459..247496057,2	MCF-7	breast:
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	chr1:247069586..247071786-chr1:247495195..247496702,2	K562	blood:
13	chr1:247495021..247495664-chr12:52444981..52445780,2	Hela-S3	cervix:
14	chr1:247495187..247495988-chr9:79008974..79009831,2	HCT-116	colon:
15	chr1:247495232..247496940-chr1:247645349..247647027,2	K562	blood:
16	chr1:247495432..247495974-chr10:77162497..77163288,2	Hela-S3	cervix:
17	chr1:247495212..247495870-chr7:102715654..102716186,2	Hela-S3	cervix:
18	chr1:247093791..247096097-chr1:247493835..247497465,5	K562	blood:
19	chr1:247495202..247495979-chr14:105219028..105219965,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NLRP3-1	chr1:247495531-247495666	NONHSAT010772
2	lnc-NLRP3-1	chr1:247495187-247498708	NONHSAT010771

Variant related genes	Relation type
ZNF496	TF binding region
ENSG00000184990	Chromatin interaction
ENSG00000135747	Chromatin interaction
ENSG00000188295	Chromatin interaction
ENSG00000135002	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000237149	Chromatin interaction
ENSG00000227671	Chromatin interaction
ENSG00000153207	Chromatin interaction
ENSG00000174851	Chromatin interaction
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:19 , 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	esv1848384	chr1:247485654-247495666	Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
6	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
7	esv1811709	chr1:247491143-247495666	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
8	esv1840501	chr1:247491143-247495666	Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
9	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
10	esv17401	chr1:247494711-247495773	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
11	nsv549588	chr1:247494738-247495666	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
12	nsv549589	chr1:247494738-247495693	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
13	nsv549591	chr1:247494789-247495666	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
14	nsv549592	chr1:247494789-247495693	Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
15	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
16	nsv549593	chr1:247494841-247495693	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
17	nsv549594	chr1:247494893-247495693	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
18	nsv549595	chr1:247494944-247495693	Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
19	nsv549596	chr1:247494996-247495693	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 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	chr1:247493800-247495800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:247493800-247496200	Active TSS	HSMMtube	muscle
4	chr1:247493800-247496400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:247493800-247496600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:247494000-247496000	Active TSS	NHLF	lung
7	chr1:247494000-247496400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:247494000-247496400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:247494000-247496400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:247494000-247496400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:247494000-247496400	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:247494000-247496400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:247494000-247496600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:247494000-247496600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:247494200-247495800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:247494200-247495800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr1:247494200-247495800	Active TSS	Brain Angular Gyrus	brain
18	chr1:247494200-247495800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr1:247494200-247495800	Active TSS	Brain Substantia Nigra	brain
20	chr1:247494200-247495800	Active TSS	Fetal Intestine Large	intestine
21	chr1:247494200-247495800	Active TSS	Fetal Lung	lung
22	chr1:247494200-247495800	Active TSS	Fetal Stomach	stomach
23	chr1:247494200-247495800	Active TSS	Fetal Thymus	thymus
24	chr1:247494200-247495800	Active TSS	Psoas Muscle	Psoas
25	chr1:247494200-247495800	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr1:247494200-247495800	Active TSS	Thymus	Thymus
27	chr1:247494200-247495800	Active TSS	Hela-S3	cervix
28	chr1:247494200-247495800	Active TSS	HUVEC	blood vessel
29	chr1:247494200-247495800	Active TSS	K562	blood
30	chr1:247494200-247495800	Active TSS	NHDF-Ad	bronchial
31	chr1:247494200-247495800	Active TSS	NHEK	skin
32	chr1:247494200-247496000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:247494200-247496000	Active TSS	Brain Anterior Caudate	brain
34	chr1:247494200-247496000	Active TSS	Fetal Brain Female	brain
35	chr1:247494200-247496000	Active TSS	Rectal Smooth Muscle	rectum
36	chr1:247494200-247496200	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr1:247494200-247496200	Active TSS	Aorta	Aorta
38	chr1:247494200-247496200	Active TSS	Brain Cingulate Gyrus	brain
39	chr1:247494200-247496200	Active TSS	Colon Smooth Muscle	Colon
40	chr1:247494200-247496200	Active TSS	A549	lung
41	chr1:247494200-247496200	Active TSS	HSMM	muscle
42	chr1:247494200-247496400	Active TSS	H1 Cell Line	embryonic stem cell
43	chr1:247494200-247496400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:247494200-247496400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:247494200-247496400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:247494200-247496400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:247494200-247496400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:247494200-247496400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:247494200-247496400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:247494200-247496400	Active TSS	Duodenum Smooth Muscle	Duodenum

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