Variant report

Variant	rs2231993
Chromosome Location	chr19:19030689-19030690
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	MYC	chr19:19029933-19030858	HUVEC	blood vessel:	n/a	n/a
2	SP2	chr19:19030042-19030705	K562	blood:	n/a	chr19:19030248-19030271 chr19:19030357-19030367 chr19:19030265-19030275
3	TRIM28	chr19:19029550-19030742	K562	blood:	n/a	n/a
4	POLR2A	chr19:19029567-19030939	H1-neurons	neurons:	n/a	n/a
5	MAX	chr19:19029395-19030909	K562	blood:	n/a	n/a
6	USF2	chr19:19029723-19030873	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:19030381-19030813	A549	lung:	n/a	n/a
8	POLR2A	chr19:19029257-19030733	K562	blood:	n/a	n/a
9	CREB1	chr19:19029723-19030964	K562	blood:	n/a	chr19:19030474-19030487
10	CTCF	chr19:19029669-19030696	GM12878	blood:	n/a	n/a
11	GABPA	chr19:19029938-19030727	H1-hESC	embryonic stem cell:	n/a	chr19:19030008-19030017
12	MXI1	chr19:19029515-19031033	K562	blood:	n/a	n/a
13	POLR2A	chr19:19030416-19030769	HepG2	liver:	n/a	n/a
14	MYC	chr19:19029698-19031052	NB4	blood:	n/a	n/a
15	YY1	chr19:19029438-19030802	GM12878	blood:	n/a	chr19:19029990-19029999 chr19:19029991-19030005 chr19:19030647-19030667 chr19:19030018-19030029
16	USF2	chr19:19030362-19031021	K562	blood:	n/a	n/a
17	MYC	chr19:19029568-19030895	K562	blood:	n/a	n/a
18	ETS1	chr19:19029939-19030771	GM12878	blood:	n/a	chr19:19030198-19030211 chr19:19030495-19030505 chr19:19030491-19030504 chr19:19030194-19030210 chr19:19030225-19030238 chr19:19030333-19030346 chr19:19030492-19030501 chr19:19030494-19030505 chr19:19029993-19030004 chr19:19030199-19030208
19	PML	chr19:19029714-19030901	MCF-7	breast:	n/a	n/a
20	TBP	chr19:19029613-19030928	GM12878	blood:	n/a	n/a
21	TAF1	chr19:19029651-19030775	K562	blood:	n/a	n/a
22	REST	chr19:19029639-19030891	HL-60	blood:	n/a	chr19:19030410-19030423
23	SRF	chr19:19030052-19030747	ECC-1	luminal epithelium:	n/a	n/a
24	MYC	chr19:19029768-19030930	MCF10A-Er-Src	breast:	n/a	n/a
25	SRF	chr19:19029893-19030800	MCF-7	breast:	n/a	n/a
26	GABPA	chr19:19029389-19031297	MCF-7	breast:	n/a	chr19:19030008-19030017
27	SIN3AK20	chr19:19029979-19030786	HepG2	liver:	n/a	n/a
28	HCFC1	chr19:19029748-19030859	K562	blood:	n/a	n/a
29	CREB1	chr19:19029478-19031091	GM12878	blood:	n/a	chr19:19030474-19030487
30	GABPA	chr19:19029991-19030756	GM12878	blood:	n/a	chr19:19030008-19030017
31	POLR2A	chr19:19029640-19030855	Raji	blood:	n/a	n/a
32	MAZ	chr19:19029672-19030747	K562	blood:	n/a	n/a
33	POLR2A	chr19:19029557-19030975	H1-hESC	embryonic stem cell:	n/a	n/a
34	SRF	chr19:19029907-19030849	MCF-7	breast:	n/a	n/a
35	SIX5	chr19:19030038-19030726	H1-hESC	embryonic stem cell:	n/a	chr19:19030333-19030347 chr19:19030336-19030345 chr19:19030228-19030237 chr19:19030225-19030239 chr19:19030334-19030343
36	YY1	chr19:19029925-19030719	HepG2	liver:	n/a	chr19:19029990-19029999 chr19:19029991-19030005 chr19:19030647-19030667 chr19:19030018-19030029
37	MXI1	chr19:19029803-19030892	H1-hESC	embryonic stem cell:	n/a	n/a
38	ATF3	chr19:19030065-19030796	K562	blood:	n/a	chr19:19030475-19030486 chr19:19030488-19030497 chr19:19030486-19030495 chr19:19030476-19030496
39	TAF1	chr19:19029874-19030792	HepG2	liver:	n/a	n/a
40	SP2	chr19:19029937-19030731	HepG2	liver:	n/a	chr19:19030248-19030271 chr19:19030357-19030367 chr19:19030265-19030275
41	CREB1	chr19:19029813-19030751	A549	lung:	n/a	chr19:19030474-19030487
42	POLR2A	chr19:19029682-19030768	HCT-116	colon:	n/a	n/a
43	TBL1XR1	chr19:19029650-19030904	GM12878	blood:	n/a	n/a
44	YY1	chr19:19029724-19030744	SK-N-SH_RA	brain:	n/a	chr19:19029990-19029999 chr19:19029991-19030005 chr19:19030647-19030667 chr19:19030018-19030029
45	POLR2A	chr19:19029627-19030774	GM12891	blood:	n/a	n/a
46	CREB1	chr19:19029924-19030730	ECC-1	luminal epithelium:	n/a	chr19:19030474-19030487
47	MAX	chr19:19029134-19031007	K562	blood:	n/a	n/a
48	MAX	chr19:19029675-19031031	A549	lung:	n/a	n/a
49	ELF1	chr19:19029947-19030773	SK-N-SH	brain:	n/a	chr19:19030494-19030503 chr19:19029990-19029999 chr19:19030200-19030209
50	SMC3	chr19:19029562-19030900	Hela-S3	cervix:	n/a	chr19:19030439-19030449 chr19:19029995-19030005 chr19:19029971-19029978

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:19030652-19030702	AG04450	lung:	fetal
2	chr19:19030652-19030702	T-47D	breast:	n/a
3	chr19:19030652-19030702	GM12878	blood:	n/a
4	chr19:19030652-19030702	A549	lung:	n/a
5	chr19:19030652-19030702	AG10803	skin:	n/a
6	chr19:19030652-19030702	HUVEC	blood vessel:	n/a
7	chr19:19030652-19030702	Jurkat	blood:	n/a
8	chr19:19030652-19030702	AG09319	gingival:	n/a
9	chr19:19030652-19030702	Hela-S3	cervix:	n/a
10	chr19:19030652-19030702	ECC-1	luminal epithelium:	n/a
11	chr19:19030652-19030702	HNPCEpiC	eye:	n/a
12	chr19:19030652-19030702	Caco-2	colon:	n/a
13	chr19:19030652-19030702	HCF	heart:	n/a
14	chr19:19030652-19030702	SKMC	muscle:	n/a
15	chr19:19030652-19030702	HAEpiC	amniotic membrane:	n/a
16	chr19:19030652-19030702	ProgFib	skin:	n/a
17	chr19:19030652-19030702	RPTEC	kidney:	n/a
18	chr19:19030652-19030702	HCT-116	colon:	n/a
19	chr19:19030652-19030702	HEK293	kidney:	embryo
20	chr19:19030652-19030702	PFSK-1	brain:	n/a
21	chr19:19030652-19030702	HRPEpiC	eye:	n/a
22	chr19:19030652-19030702	MCF10A-Er-Src	breast:	n/a
23	chr19:19030652-19030702	BJ	skin:	n/a
24	chr19:19030652-19030702	HCPEpiC	choroid plexus:	n/a
25	chr19:19030652-19030702	HMEC	breast:	n/a
26	chr19:19030652-19030702	HIPEpiC	eye:	n/a
27	chr19:19030652-19030702	PrEC	prostate:	n/a
28	chr19:19030652-19030702	GM06990	blood:	n/a
29	chr19:19030652-19030702	GM19239	blood:	n/a
30	chr19:19030652-19030702	BE2_C	brain:	n/a
31	chr19:19030652-19030702	NHBE	bronchial:	n/a
32	chr19:19030652-19030702	PANC-1	pancreas:	n/a
33	chr19:19030652-19030702	NH-A	brain:	n/a
34	chr19:19030652-19030702	H1-hESC	embryonic stem cell:	embryo
35	chr19:19030652-19030702	NT2-D1	testis:	n/a
36	chr19:19030652-19030702	GM12892	blood:	n/a
37	chr19:19030652-19030702	SK-N-SH_RA	brain:	n/a
38	chr19:19030652-19030702	SK-N-SH	brain:	n/a
39	chr19:19030652-19030702	K562	blood:	n/a
40	chr19:19030652-19030702	AoSMC	blood vessel:	n/a
41	chr19:19030652-19030702	HEEpiC	esophagus:	n/a
42	chr19:19030652-19030702	U87	brain:	n/a
43	chr19:19030652-19030702	IMR90	lung:	fetal
44	chr19:19030652-19030702	AG04449	skin:	fetal
45	chr19:19030652-19030702	ovcar-3	ovarian:	n/a
46	chr19:19030652-19030702	SAEC	small airway:	n/a
47	chr19:19030652-19030702	HPAEpiC	pulmonary alveolar:	n/a
48	chr19:19030652-19030702	HRE	kidney:	n/a
49	chr19:19030652-19030702	HRCEpiC	kidney:	n/a
50	chr19:19030652-19030702	HepG2	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19014514..19025012-chr19:19028545..19031608,12	MCF-7	breast:
2	chr17:62221757..62224608-chr19:19030239..19032078,2	MCF-7	breast:
3	chr19:19028307..19038067-chr19:19048419..19054729,15	MCF-7	breast:
4	chr19:19028142..19040542-chr19:19046967..19057144,34	MCF-7	breast:
5	chr19:18699463..18701468-chr19:19028694..19031158,3	K562	blood:
6	chr19:19005129..19007826-chr19:19028734..19032982,4	MCF-7	breast:
7	chr19:18555810..18558424-chr19:19028708..19031515,2	K562	blood:
8	chr19:18942543..18946544-chr19:19028586..19032596,4	MCF-7	breast:
9	chr19:19028947..19031173-chr19:19514626..19517474,2	K562	blood:
10	chr19:19005501..19008972-chr19:19028688..19032169,4	K562	blood:
11	chr19:18699463..18701468-chr19:19028694..19031158,2	K562	blood:
12	chr19:19010579..19012422-chr19:19029682..19031277,2	K562	blood:
13	chr17:58602348..58605057-chr19:19030634..19032136,2	MCF-7	breast:
14	chr19:19023442..19028090-chr19:19028276..19032184,6	MCF-7	breast:
15	chr19:19030312..19031078-chr3:112359710..112360246,2	Hela-S3	cervix:
16	chr19:19028019..19031021-chr19:19142402..19146031,5	K562	blood:
17	chr19:19028699..19031698-chr19:19049211..19052149,3	K562	blood:

Variant related genes	Relation type
DDX49	TF binding region
COPE	TF binding region
COPE	CpG island
DDX49	CpG island
ENSG00000266402	Chromatin interaction
ENSG00000167491	Chromatin interaction
ENSG00000005007	Chromatin interaction
ENSG00000130283	Chromatin interaction
ENSG00000064607	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000105676	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000269019	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000051128	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000223802	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000105669	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10330	0.85[AMR][1000 genomes]
rs2106660	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158004	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2872205	1.00[ASN][1000 genomes]
rs55988241	0.82[EUR][1000 genomes]
rs7250615	0.86[EUR][1000 genomes]
rs73003085	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73003087	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73003090	0.85[EUR][1000 genomes]
rs999454	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription 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	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv470132	chr19:18964442-19054720	Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv911301	chr19:18994638-19077385	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911302	chr19:18995201-19088981	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
11	nsv543926	chr19:19029529-19062771	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 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	chr19:19028600-19031000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr19:19028600-19031400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:19028800-19031000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:19028800-19031000	Active TSS	Colon Smooth Muscle	Colon
5	chr19:19028800-19031000	Active TSS	HMEC	breast
6	chr19:19028800-19031200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:19028800-19031200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:19028800-19031200	Active TSS	GM12878-XiMat	blood
9	chr19:19028800-19031200	Active TSS	K562	blood
10	chr19:19029000-19031000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr19:19029000-19031000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:19029000-19031000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:19029000-19031000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:19029000-19031000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr19:19029000-19031200	Active TSS	Right Atrium	heart
16	chr19:19029000-19031200	Active TSS	HSMM	muscle
17	chr19:19029000-19031200	Active TSS	NHDF-Ad	bronchial
18	chr19:19029000-19031200	Active TSS	NHLF	lung
19	chr19:19029000-19031400	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr19:19029000-19031600	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr19:19029200-19030800	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr19:19029200-19031000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:19029200-19031000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:19029200-19031000	Active TSS	Esophagus	oesophagus
25	chr19:19029200-19031000	Active TSS	Fetal Intestine Large	intestine
26	chr19:19029200-19031000	Active TSS	Gastric	stomach
27	chr19:19029200-19031000	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr19:19029200-19031000	Active TSS	Small Intestine	intestine
29	chr19:19029200-19031200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr19:19029200-19031200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr19:19029200-19031200	Active TSS	H9 Cell Line	embryonic stem cell
32	chr19:19029200-19031200	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr19:19029200-19031200	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr19:19029200-19031200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:19029200-19031200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:19029200-19031200	Active TSS	Muscle Satellite Cultured Cells	--
37	chr19:19029200-19031200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:19029200-19031200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:19029200-19031200	Active TSS	Fetal Kidney	kidney
40	chr19:19029200-19031200	Active TSS	Ovary	ovary
41	chr19:19029200-19031200	Active TSS	Pancreas	Pancrea
42	chr19:19029200-19031200	Active TSS	Psoas Muscle	Psoas
43	chr19:19029200-19031200	Active TSS	HSMMtube	muscle
44	chr19:19029200-19031600	Active TSS	A549	lung
45	chr19:19029400-19030800	Active TSS	HUVEC	blood vessel
46	chr19:19029400-19031000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr19:19029400-19031000	Active TSS	Aorta	Aorta
48	chr19:19029400-19031000	Active TSS	Stomach Mucosa	stomach
49	chr19:19029400-19031000	Active TSS	NH-A	brain
50	chr19:19029400-19031200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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