Variant report

Variant	rs73015649
Chromosome Location	chr3:158450298-158450299
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	chr3:158449553-158450806	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:158449747-158450300	HUVEC	blood vessel:	n/a	n/a
3	E2F6	chr3:158449150-158450961	H1-hESC	embryonic stem cell:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
4	MAX	chr3:158449465-158450931	A549	lung:	n/a	chr3:158449551-158449560
5	GABPA	chr3:158450185-158450529	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr3:158449462-158450902	Hela-S3	cervix:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
7	RFX5	chr3:158449565-158450713	Hela-S3	cervix:	n/a	n/a
8	MAX	chr3:158449639-158450457	A549	lung:	n/a	n/a
9	CEBPB	chr3:158449669-158450932	Hela-S3	cervix:	n/a	n/a
10	HA-E2F1	chr3:158449673-158450554	Hela-S3	cervix:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
11	TCF7L2	chr3:158449320-158450575	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:158449725-158450339	A549	lung:	n/a	n/a
13	E2F6	chr3:158449465-158450823	A549	lung:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450469-158450481 chr3:158449768-158449778
14	CHD2	chr3:158449479-158450848	Hela-S3	cervix:	n/a	n/a
15	MAX	chr3:158449653-158450944	H1-hESC	embryonic stem cell:	n/a	n/a
16	SIN3A	chr3:158449403-158450925	H1-hESC	embryonic stem cell:	n/a	n/a
17	BACH1	chr3:158449772-158450885	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:158450294-158450757	Hela-S3	cervix:	n/a	n/a
19	MAX	chr3:158449524-158450747	Hela-S3	cervix:	n/a	chr3:158449551-158449560
20	E2F1	chr3:158449687-158450376	Hela-S3	cervix:	n/a	chr3:158450363-158450370 chr3:158450363-158450370 chr3:158450363-158450370 chr3:158449768-158449778
21	MAZ	chr3:158449671-158450610	Hela-S3	cervix:	n/a	n/a
22	MXI1	chr3:158449197-158450673	IMR90	lung:	n/a	n/a
23	SMARCB1	chr3:158449378-158450980	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr3:158449549-158450832	A549	lung:	n/a	chr3:158449859-158449866 chr3:158449637-158449644
25	CTBP2	chr3:158449569-158450925	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr3:158449500-158450763	A549	lung:	n/a	chr3:158449551-158449560
27	TBP	chr3:158449778-158450917	H1-hESC	embryonic stem cell:	n/a	n/a
28	GATA1	chr3:158449763-158451117	PBDE	blood:	n/a	n/a
29	ZNF143	chr3:158450198-158450393	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:158449639-158450511	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr3:158449618-158450683	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr3:158449667-158450584	A549	lung:	n/a	n/a
33	CEBPB	chr3:158450163-158451018	A549	lung:	n/a	n/a
34	PAX5	chr3:158449790-158450342	GM12892	blood:	n/a	n/a
35	MAX	chr3:158449347-158451065	H1-hESC	embryonic stem cell:	n/a	chr3:158449551-158449560
36	POLR2A	chr3:158449739-158450304	A549	lung:	n/a	n/a
37	CEBPB	chr3:158450295-158450797	A549	lung:	n/a	n/a
38	POLR2A	chr3:158449712-158450652	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:158449252-158450772	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr3:158450200-158450581	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:158450251-158450301	SAEC	small airway:	n/a
2	chr3:158450251-158450301	HRCEpiC	kidney:	n/a
3	chr3:158450251-158450301	HCF	heart:	n/a
4	chr3:158450251-158450301	A549	lung:	n/a
5	chr3:158450251-158450301	Hepatocyte	liver:	n/a
6	chr3:158450251-158450301	AoSMC	blood vessel:	n/a
7	chr3:158450251-158450301	ovcar-3	ovarian:	n/a
8	chr3:158450251-158450301	AG04450	lung:	fetal
9	chr3:158450251-158450301	HRPEpiC	eye:	n/a
10	chr3:158450251-158450301	NB4	blood:	n/a
11	chr3:158450251-158450301	Jurkat	blood:	n/a
12	chr3:158450251-158450301	RPTEC	kidney:	n/a
13	chr3:158450251-158450301	AG10803	skin:	n/a
14	chr3:158450251-158450301	IMR90	lung:	fetal
15	chr3:158450251-158450301	Caco-2	colon:	n/a
16	chr3:158450251-158450301	SK-N-SH_RA	brain:	n/a
17	chr3:158450251-158450301	HCT-116	colon:	n/a
18	chr3:158450251-158450301	HRE	kidney:	n/a
19	chr3:158450251-158450301	SKMC	muscle:	n/a
20	chr3:158450251-158450301	GM06990	blood:	n/a
21	chr3:158450251-158450301	ProgFib	skin:	n/a
22	chr3:158450251-158450301	NT2-D1	testis:	n/a
23	chr3:158450251-158450301	PFSK-1	brain:	n/a
24	chr3:158450251-158450301	HUVEC	blood vessel:	n/a
25	chr3:158450251-158450301	AG09319	gingival:	n/a
26	chr3:158450251-158450301	PANC-1	pancreas:	n/a
27	chr3:158450251-158450301	BJ	skin:	n/a
28	chr3:158450251-158450301	HCPEpiC	choroid plexus:	n/a
29	chr3:158450251-158450301	HNPCEpiC	eye:	n/a
30	chr3:158450251-158450301	HMEC	breast:	n/a
31	chr3:158450251-158450301	GM12878	blood:	n/a
32	chr3:158450251-158450301	U87	brain:	n/a
33	chr3:158450251-158450301	MCF10A-Er-Src	breast:	n/a
34	chr3:158450251-158450301	NH-A	brain:	n/a
35	chr3:158450251-158450301	HIPEpiC	eye:	n/a
36	chr3:158450251-158450301	GM12891	blood:	n/a
37	chr3:158450251-158450301	SK-N-MC	brain:	n/a
38	chr3:158450251-158450301	K562	blood:	n/a
39	chr3:158450251-158450301	AG04449	skin:	fetal
40	chr3:158450251-158450301	HepG2	liver:	n/a
41	chr3:158450251-158450301	GM19239	blood:	n/a
42	chr3:158450251-158450301	NHBE	bronchial:	n/a
43	chr3:158450251-158450301	BE2_C	brain:	n/a
44	chr3:158450251-158450301	ECC-1	luminal epithelium:	n/a
45	chr3:158450251-158450301	SK-N-SH	brain:	n/a
46	chr3:158450251-158450301	HEEpiC	esophagus:	n/a
47	chr3:158450251-158450301	HCM	heart:	n/a
48	chr3:158450251-158450301	MCF-7	breast:	n/a
49	chr3:158450251-158450301	HEK293	kidney:	embryo
50	chr3:158450251-158450301	LNCaP	prostate:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158449938..158451943-chr3:158452978..158454973,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GFM1-1	chr3:158450167-158450317	ENSG00000240207.1
2	lnc-GFM1-1	chr3:158450116-158450317	ENSG00000240207.1
3	lnc-GFM1-1	chr3:158450052-158450317	ENSG00000240207.2

Variant related genes	Relation type
RARRES1	TF binding region
ENSG00000240207	TF binding region
ENSG00000240207	CpG island
RARRES1	CpG island
ENSG00000240207	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs59217052	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59313096	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59918529	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61387735	0.95[AFR][1000 genomes]
rs61558956	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61696028	0.95[AFR][1000 genomes]
rs6441222	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73015651	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73015652	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73015654	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73015655	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73015657	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73015669	0.93[AFR][1000 genomes]
rs7609656	0.83[EUR][1000 genomes]
rs7621322	0.89[EUR][1000 genomes]
rs7646881	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7646987	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449000-158450600	Active TSS	Sigmoid Colon	Sigmoid Colon
2	chr3:158449000-158450800	Flanking Active TSS	NH-A	brain
3	chr3:158449000-158451000	Active TSS	Fetal Kidney	kidney
4	chr3:158449200-158450800	Active TSS	Brain Anterior Caudate	brain
5	chr3:158449200-158450800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr3:158449200-158451000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:158449200-158451000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:158449400-158450400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr3:158449400-158450400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
10	chr3:158449400-158450600	Active TSS	HSMM	muscle
11	chr3:158449400-158450600	Flanking Active TSS	HUVEC	blood vessel
12	chr3:158449400-158450800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:158449400-158450800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:158449400-158450800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr3:158449400-158450800	Active TSS	Small Intestine	intestine
16	chr3:158449400-158450800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
17	chr3:158449400-158451000	Active TSS	H9 Cell Line	embryonic stem cell
18	chr3:158449400-158451000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr3:158449400-158451000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:158449400-158451000	Flanking Active TSS	Right Ventricle	heart
21	chr3:158449600-158450400	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr3:158449600-158450400	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr3:158449600-158450400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:158449600-158450400	Active TSS	Colonic Mucosa	Colon
25	chr3:158449600-158450400	Active TSS	Fetal Intestine Small	intestine
26	chr3:158449600-158450400	Active TSS	Left Ventricle	heart
27	chr3:158449600-158450600	Enhancers	Primary B cells from peripheral blood	blood
28	chr3:158449600-158450600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:158449600-158450600	Flanking Active TSS	HMEC	breast
30	chr3:158449600-158450600	Active TSS	NHDF-Ad	bronchial
31	chr3:158449600-158450800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:158449600-158450800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr3:158449600-158450800	Active TSS	Aorta	Aorta
34	chr3:158449600-158450800	Active TSS	Psoas Muscle	Psoas
35	chr3:158449600-158451000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr3:158449600-158451000	Active TSS	Esophagus	oesophagus
37	chr3:158449600-158451000	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr3:158449600-158451600	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr3:158449800-158450400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:158449800-158450400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:158449800-158450400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:158449800-158450400	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr3:158449800-158450400	Active TSS	Adipose Nuclei	Adipose
44	chr3:158449800-158450400	Active TSS	Fetal Muscle Leg	muscle
45	chr3:158449800-158450400	Bivalent/Poised TSS	Fetal Stomach	stomach
46	chr3:158449800-158450400	Active TSS	GM12878-XiMat	blood
47	chr3:158449800-158450400	Active TSS	HSMMtube	muscle
48	chr3:158449800-158450400	Active TSS	NHLF	lung
49	chr3:158449800-158450600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:158449800-158450600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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