Variant report

Variant	rs73000320
Chromosome Location	chr1:113499320-113499321
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	chr1:113497956-113499458	Gliobla	brain:	n/a	n/a
2	POLR2A	chr1:113497811-113500745	SK-N-MC	brain:	n/a	n/a
3	MYC	chr1:113498017-113499374	H1-hESC	embryonic stem cell:	n/a	chr1:113498500-113498509
4	MAX	chr1:113497708-113499464	A549	lung:	n/a	chr1:113498500-113498509
5	POLR2A	chr1:113498518-113500821	GM12891	blood:	n/a	n/a
6	MYC	chr1:113497412-113500450	K562	blood:	n/a	chr1:113497413-113497426 chr1:113497413-113497426 chr1:113497417-113497424 chr1:113497414-113497425 chr1:113500276-113500286 chr1:113497414-113497425 chr1:113497415-113497424 chr1:113497413-113497426 chr1:113497415-113497425 chr1:113497416-113497425 chr1:113497557-113497566 chr1:113497414-113497425 chr1:113498500-113498509
7	BHLHE40	chr1:113497739-113499385	K562	blood:	n/a	chr1:113497989-113498005
8	E2F1	chr1:113498524-113499428	Hela-S3	cervix:	n/a	chr1:113498897-113498907 chr1:113498939-113498948
9	POLR2A	chr1:113497733-113500665	U87	brain:	n/a	n/a
10	POLR2A	chr1:113497768-113500702	Hela-S3	cervix:	n/a	n/a
11	MAX	chr1:113497807-113499376	ECC-1	luminal epithelium:	n/a	chr1:113498500-113498509
12	SMARCB1	chr1:113497822-113499826	Hela-S3	cervix:	n/a	n/a
13	USF1	chr1:113498603-113499356	HCT-116	colon:	n/a	chr1:113499007-113499018
14	POLR2A	chr1:113498422-113499598	ProgFib	skin:	n/a	n/a
15	SIN3AK20	chr1:113497791-113499576	SK-N-SH	brain:	n/a	n/a
16	USF1	chr1:113498625-113499352	SK-N-SH	brain:	n/a	chr1:113499007-113499018
17	MXI1	chr1:113497254-113500450	Hela-S3	cervix:	n/a	n/a
18	TAF1	chr1:113498543-113499769	GM12878	blood:	n/a	n/a
19	CBX3	chr1:113497783-113499370	K562	blood:	n/a	n/a
20	POLR2A	chr1:113497698-113499417	K562	blood:	n/a	n/a
21	FOS	chr1:113498766-113499395	HUVEC	blood vessel:	n/a	n/a
22	KAP1	chr1:113497751-113499419	HEK293	kidney:	n/a	n/a
23	RUNX3	chr1:113497744-113499513	GM12878	blood:	n/a	n/a
24	E2F4	chr1:113498645-113499432	MCF10A-Er-Src	breast:	n/a	chr1:113498897-113498907 chr1:113498939-113498948
25	RELA	chr1:113497818-113499509	GM15510	blood:	n/a	n/a
26	EBF1	chr1:113497916-113499544	GM12878	blood:	n/a	chr1:113498237-113498246 chr1:113498236-113498246
27	POLR2A	chr1:113497957-113500404	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:113497823-113499386	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr1:113497842-113500826	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:113497822-113500697	GM12892	blood:	n/a	n/a
31	POLR2A	chr1:113497758-113500619	IMR90	lung:	n/a	n/a
32	E2F6	chr1:113497917-113500218	K562	blood:	n/a	chr1:113498897-113498907 chr1:113498939-113498948
33	POLR2A	chr1:113497767-113500708	GM12891	blood:	n/a	n/a
34	POLR2A	chr1:113497890-113500482	Raji	blood:	n/a	n/a
35	CEBPD	chr1:113498540-113499364	K562	blood:	n/a	n/a
36	MAX	chr1:113497762-113499401	SK-N-SH	brain:	n/a	chr1:113498500-113498509
37	USF1	chr1:113498621-113499322	A549	lung:	n/a	chr1:113499007-113499018
38	POLR2A	chr1:113497929-113500488	GM18526	blood:	n/a	n/a
39	POLR2A	chr1:113497779-113500342	K562	blood:	n/a	n/a
40	POLR2A	chr1:113498305-113499453	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr1:113497918-113500595	GM12878	blood:	n/a	n/a
42	TEAD4	chr1:113497330-113499433	K562	blood:	n/a	n/a
43	HEY1	chr1:113498333-113500499	HepG2	liver:	n/a	n/a
44	ZBTB7A	chr1:113497741-113499372	ECC-1	luminal epithelium:	n/a	n/a
45	RELA	chr1:113497803-113499420	GM10847	blood:	n/a	n/a
46	POLR2A	chr1:113497835-113500199	K562	blood:	n/a	n/a
47	POLR2A	chr1:113497862-113499443	K562	blood:	n/a	n/a
48	YY1	chr1:113497834-113499411	K562	blood:	n/a	chr1:113498061-113498075 chr1:113498893-113498904 chr1:113498899-113498908 chr1:113498897-113498911 chr1:113498896-113498905
49	POLR2A	chr1:113498488-113499352	HUVEC	blood vessel:	n/a	n/a
50	YY1	chr1:113498200-113499394	GM12878	blood:	n/a	chr1:113498893-113498904 chr1:113498899-113498908 chr1:113498897-113498911 chr1:113498896-113498905

No.	Distal block	Cell Line	Cell type
1	chr1:113459369..113469193-chr1:113493855..113500263,12	K562	blood:
2	chr1:113499016..113499759-chr22:19419436..19420248,2	Hela-S3	cervix:
3	chr1:113255626..113260544-chr1:113496476..113500122,4	K562	blood:
4	chr1:113476800..113479671-chr1:113497569..113500244,3	MCF-7	breast:
5	chr1:113161304..113162931-chr1:113498706..113500285,2	K562	blood:
6	chr1:43423856..43424635-chr1:113498800..113499582,2	Hela-S3	cervix:
7	chr1:113498819..113501560-chr8:144951768..144953643,2	MCF-7	breast:
8	chr1:113476476..113482692-chr1:113494893..113501777,18	K562	blood:
9	chr1:113498522..113499498-chr6:153304465..153305398,2	Hela-S3	cervix:
10	chr1:113495059..113500488-chr1:113613593..113618010,11	K562	blood:
11	chr1:113498943..113499617-chr17:73775476..73776075,2	Hela-S3	cervix:
12	chr1:113493791..113500715-chr1:113613796..113618010,15	K562	blood:
13	chr1:113498236..113500475-chr17:56707428..56710139,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRIG2-4	chr1:113499083-113500344	ENSG00000226419
2	lnc-LRIG2-4	chr1:113499142-113499578	ENSG00000226419
3	lnc-LRIG2-4	chr1:113499037-113499578	ENSG00000226419
4	lnc-LRIG2-4	chr1:113499051-113499578	ENSG00000226419
5	lnc-LRIG2-3	chr1:113499185-113499578	NONHSAT005303
6	lnc-LRIG2-3	chr1:113499037-113499578	NR_103744
7	lnc-LRIG2-3	chr1:113499037-113499578	NONHSAT005299
8	lnc-LRIG2-3	chr1:113499051-113499578	ENSG00000226419.2
9	lnc-LRIG2-3	chr1:113499037-113500344	NONHSAT005297
10	lnc-LRIG2-3	chr1:113499232-113499578	NONHSAT005304

Variant related genes	Relation type
SLC16A1	TF binding region
ENSG00000238198	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000112029	Chromatin interaction
ENSG00000227184	Chromatin interaction
ENSG00000229020	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000227627	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000198799	Chromatin interaction
ENSG00000117394	Chromatin interaction
ENSG00000185608	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11102561	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805071	0.84[AFR][1000 genomes]
rs12071491	1.00[ASN][1000 genomes]
rs12117273	1.00[ASN][1000 genomes]
rs12123072	1.00[ASN][1000 genomes]
rs12123519	1.00[ASN][1000 genomes]
rs12126316	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133057	1.00[ASN][1000 genomes]
rs12137299	1.00[ASN][1000 genomes]
rs12138968	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140067	1.00[ASN][1000 genomes]
rs12141018	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141415	1.00[ASN][1000 genomes]
rs12143171	1.00[ASN][1000 genomes]
rs12143341	1.00[ASN][1000 genomes]
rs12184272	1.00[ASN][1000 genomes]
rs12184320	1.00[ASN][1000 genomes]
rs12744661	1.00[ASN][1000 genomes]
rs41306207	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56335344	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57793802	0.88[AFR][1000 genomes]
rs6665673	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982435	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982438	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73000335	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535389	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541119	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545814	1.00[ASN][1000 genomes]
rs9429503	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
14	esv1827123	chr1:113496841-113531848	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 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	chr1:113495200-113501400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:113495800-113500200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:113495800-113500600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:113495800-113500600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:113495800-113500800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:113495800-113501400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:113496000-113501000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:113496200-113500400	Active TSS	Stomach Smooth Muscle	stomach
9	chr1:113496200-113501800	Active TSS	Right Ventricle	heart
10	chr1:113496400-113500000	Active TSS	Psoas Muscle	Psoas
11	chr1:113496400-113500600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr1:113496400-113500600	Active TSS	Aorta	Aorta
13	chr1:113496400-113501400	Active TSS	GM12878-XiMat	blood
14	chr1:113496600-113500400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:113496600-113500800	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr1:113496600-113501400	Active TSS	Rectal Smooth Muscle	rectum
17	chr1:113496600-113501400	Active TSS	HepG2	liver
18	chr1:113496600-113501600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:113496800-113499600	Active TSS	Fetal Thymus	thymus
20	chr1:113496800-113500000	Active TSS	Fetal Brain Female	brain
21	chr1:113496800-113500200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr1:113496800-113500200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:113496800-113500200	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr1:113496800-113500200	Active TSS	HSMM	muscle
25	chr1:113496800-113500400	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr1:113496800-113500400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:113496800-113500400	Active TSS	HMEC	breast
28	chr1:113496800-113500600	Active TSS	H1 Cell Line	embryonic stem cell
29	chr1:113496800-113500600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:113497000-113499800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:113497000-113499800	Active TSS	Hela-S3	cervix
32	chr1:113497000-113500200	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr1:113497000-113500400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:113497000-113500400	Active TSS	Fetal Stomach	stomach
35	chr1:113497000-113500600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:113497000-113500600	Active TSS	Ovary	ovary
37	chr1:113497000-113500600	Active TSS	HSMMtube	muscle
38	chr1:113497200-113499400	Active TSS	K562	blood
39	chr1:113497200-113499800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:113497200-113499800	Active TSS	Duodenum Mucosa	Duodenum
41	chr1:113497200-113500000	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr1:113497200-113500400	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr1:113497200-113500400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:113497200-113500400	Active TSS	A549	lung
45	chr1:113497200-113500400	Active TSS	NHDF-Ad	bronchial
46	chr1:113497200-113500400	Active TSS	NHEK	skin
47	chr1:113497200-113500600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:113497200-113500600	Active TSS	Fetal Intestine Large	intestine
49	chr1:113497200-113500600	Active TSS	NHLF	lung
50	chr1:113497200-113501200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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