Variant report

Variant	rs7594264
Chromosome Location	chr2:38829488-38829489
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	chr2:38828488-38830465	H1-hESC	embryonic stem cell:	n/a	n/a
2	GABPA	chr2:38829345-38830587	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:38829453-38830716	PFSK-1	brain:	n/a	n/a
4	SIN3AK20	chr2:38829163-38830978	SK-N-SH	brain:	n/a	n/a
5	UBTF	chr2:38828546-38830909	K562	blood:	n/a	n/a
6	MAX	chr2:38829019-38831087	HepG2	liver:	n/a	n/a
7	RCOR1	chr2:38828426-38831063	IMR90	lung:	n/a	n/a
8	YY1	chr2:38829427-38830288	H1-hESC	embryonic stem cell:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
9	YY1	chr2:38829344-38830866	GM12878	blood:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
10	SIN3AK20	chr2:38828533-38831144	MCF-7	breast:	n/a	n/a
11	CHD2	chr2:38829207-38830825	Hela-S3	cervix:	n/a	n/a
12	YY1	chr2:38829237-38830294	ECC-1	luminal epithelium:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
13	TAF1	chr2:38829302-38830510	K562	blood:	n/a	n/a
14	ZBTB7A	chr2:38828985-38830833	ECC-1	luminal epithelium:	n/a	n/a
15	EGR1	chr2:38829402-38831083	HCT-116	colon:	n/a	chr2:38830139-38830152 chr2:38830140-38830149 chr2:38830134-38830156 chr2:38829801-38829811 chr2:38830139-38830152 chr2:38830138-38830153 chr2:38830139-38830152 chr2:38830138-38830152 chr2:38830139-38830149 chr2:38829798-38829811 chr2:38830140-38830151 chr2:38830139-38830152 chr2:38830136-38830150
16	TAF1	chr2:38829445-38830249	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr2:38828985-38830918	H1-neurons	neurons:	n/a	n/a
18	MAX	chr2:38829399-38831046	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr2:38829066-38830968	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr2:38829243-38830369	HL-60	blood:	n/a	n/a
21	CTCF	chr2:38829340-38829490	Caco-2	colon:	n/a	n/a
22	YY1	chr2:38829104-38830330	H1-hESC	embryonic stem cell:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
23	TCF12	chr2:38828537-38831166	A549	lung:	n/a	n/a
24	RAD21	chr2:38827547-38831481	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr2:38829316-38830677	Hela-S3	cervix:	n/a	n/a
26	HEY1	chr2:38829004-38830548	K562	blood:	n/a	chr2:38829898-38829913 chr2:38830197-38830212
27	MAX	chr2:38829039-38831033	HepG2	liver:	n/a	n/a
28	ELF1	chr2:38829487-38830465	GM12878	blood:	n/a	chr2:38829853-38829862 chr2:38830084-38830097 chr2:38829849-38829858 chr2:38829770-38829782
29	SIN3AK20	chr2:38829447-38831007	MCF-7	breast:	n/a	n/a
30	CCNT2	chr2:38829100-38830931	K562	blood:	n/a	n/a
31	TAF1	chr2:38829374-38830551	A549	lung:	n/a	n/a
32	HEY1	chr2:38828474-38830907	HepG2	liver:	n/a	chr2:38829898-38829913 chr2:38830197-38830212
33	POLR2A	chr2:38829371-38830785	HepG2	liver:	n/a	n/a
34	POLR2A	chr2:38828579-38830561	K562	blood:	n/a	n/a
35	MAX	chr2:38829209-38831045	A549	lung:	n/a	n/a
36	YY1	chr2:38829156-38830520	K562	blood:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
37	YY1	chr2:38829291-38830197	K562	blood:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
38	GATA3	chr2:38829361-38831106	A549	lung:	n/a	n/a
39	SPI1	chr2:38829204-38830491	HL-60	blood:	n/a	chr2:38830015-38830028
40	YY1	chr2:38829214-38830367	SK-N-SH	brain:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
41	YY1	chr2:38829313-38830906	GM12892	blood:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
42	POLR2A	chr2:38829007-38830825	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr2:38829344-38830432	ProgFib	skin:	n/a	n/a
44	TAF1	chr2:38829291-38830533	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr2:38829326-38829490	SK-N-SH	brain:	n/a	n/a
46	REST	chr2:38828498-38831160	H1-neurons	neurons:	n/a	chr2:38830014-38830027 chr2:38829373-38829386 chr2:38830026-38830039 chr2:38829806-38829819
47	ZNF263	chr2:38829152-38830968	HEK293-T-REx	kidney:	n/a	chr2:38830099-38830108 chr2:38830012-38830033 chr2:38830020-38830029 chr2:38830023-38830032
48	MAZ	chr2:38829414-38830970	HepG2	liver:	n/a	n/a
49	MAX	chr2:38829313-38830907	MCF-7	breast:	n/a	n/a
50	TAF1	chr2:38829395-38830864	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38827534..38829774-chr2:38906960..38909388,3	K562	blood:
2	chr11:62622751..62623580-chr2:38829450..38830201,2	Hela-S3	cervix:
3	chr2:38828577..38831705-chr2:38976861..38979916,6	MCF-7	breast:
4	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
5	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
6	chr2:38823060..38827854-chr2:38827983..38831423,11	MCF-7	breast:
7	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
8	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
9	chr2:38816751..38822030-chr2:38827238..38830922,5	MCF-7	breast:
10	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
11	chr2:38821957..38830238-chr2:38965333..38974515,17	K562	blood:
12	chr2:38816590..38821819-chr2:38825503..38830021,9	MCF-7	breast:

Variant related genes	Relation type
HNRNPLL	TF binding region
ENSG00000168003	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000232518	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000143889	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1543880	0.85[AMR][1000 genomes]
rs17022945	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs41446253	0.85[AMR][1000 genomes]
rs55773228	0.92[AFR][1000 genomes]
rs55820712	0.84[AFR][1000 genomes]
rs55957936	0.85[AMR][1000 genomes]
rs56251362	0.85[AMR][1000 genomes]
rs59114683	0.85[AMR][1000 genomes]
rs60475078	0.85[AMR][1000 genomes]
rs6710613	0.83[AFR][1000 genomes]
rs6727765	0.85[AMR][1000 genomes]
rs6732743	0.85[AMR][1000 genomes]
rs6748685	0.86[AFR][1000 genomes]
rs72897608	0.85[AMR][1000 genomes]
rs72897610	0.85[AMR][1000 genomes]
rs72905837	0.85[AMR][1000 genomes]
rs72905843	0.85[AMR][1000 genomes]
rs72905844	0.85[AMR][1000 genomes]
rs72905847	0.85[AMR][1000 genomes]
rs72905861	0.85[AMR][1000 genomes]
rs72905863	0.85[AMR][1000 genomes]
rs72905868	0.85[AMR][1000 genomes]
rs72905869	0.85[AMR][1000 genomes]
rs72905871	0.85[AMR][1000 genomes]
rs72905880	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72907906	0.81[AFR][1000 genomes]
rs72907918	0.86[AFR][1000 genomes]
rs72907929	0.83[AFR][1000 genomes]
rs73929050	0.85[AMR][1000 genomes]
rs73929077	0.85[AMR][1000 genomes]
rs73929087	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73931606	0.82[AFR][1000 genomes]
rs7579589	0.82[AFR][1000 genomes]
rs7580657	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr2:38822800-38830400	Active TSS	Primary T cells fromperipheralblood	blood
2	chr2:38825000-38830600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:38825200-38831000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:38825600-38830800	Active TSS	Stomach Smooth Muscle	stomach
5	chr2:38826200-38830800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:38826400-38830600	Active TSS	K562	blood
7	chr2:38826400-38831400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:38826800-38830600	Active TSS	NHLF	lung
9	chr2:38826800-38831000	Active TSS	Duodenum Mucosa	Duodenum
10	chr2:38827000-38830600	Active TSS	Aorta	Aorta
11	chr2:38827000-38830800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:38827000-38830800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:38827000-38830800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:38827000-38830800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:38827000-38831400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr2:38827200-38830400	Active TSS	HMEC	breast
17	chr2:38827200-38830600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr2:38827200-38830600	Active TSS	NH-A	brain
19	chr2:38827200-38830800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:38827200-38830800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr2:38827200-38830800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:38827200-38830800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:38827200-38830800	Active TSS	Fetal Intestine Small	intestine
24	chr2:38827200-38831000	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr2:38827200-38831000	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr2:38827200-38831000	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr2:38827200-38831200	Active TSS	Brain Germinal Matrix	brain
28	chr2:38827400-38830600	Active TSS	Fetal Stomach	stomach
29	chr2:38827400-38830800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr2:38827400-38830800	Active TSS	H9 Cell Line	embryonic stem cell
31	chr2:38827400-38830800	Bivalent/Poised TSS	HepG2	liver
32	chr2:38827400-38831000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr2:38827400-38831000	Active TSS	Right Ventricle	heart
34	chr2:38827400-38831200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:38827600-38830600	Active TSS	Colon Smooth Muscle	Colon
36	chr2:38827600-38830800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:38827600-38830800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr2:38827600-38830800	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr2:38827600-38830800	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr2:38827600-38830800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:38827600-38830800	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr2:38827600-38830800	Active TSS	Brain Angular Gyrus	brain
43	chr2:38827600-38830800	Active TSS	HSMM	muscle
44	chr2:38827600-38831000	Active TSS	Brain Anterior Caudate	brain
45	chr2:38827600-38831000	Active TSS	Thymus	Thymus
46	chr2:38827600-38831400	Active TSS	Colonic Mucosa	Colon
47	chr2:38827800-38830600	Active TSS	Hela-S3	cervix
48	chr2:38827800-38830800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:38827800-38830800	Active TSS	Muscle Satellite Cultured Cells	--
50	chr2:38827800-38830800	Active TSS	Esophagus	oesophagus

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