Variant report

Variant	rs6745023
Chromosome Location	chr2:38829395-38829396
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	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	SIN3AK20	chr2:38829163-38830978	SK-N-SH	brain:	n/a	n/a
4	UBTF	chr2:38828546-38830909	K562	blood:	n/a	n/a
5	MAX	chr2:38829019-38831087	HepG2	liver:	n/a	n/a
6	RCOR1	chr2:38828426-38831063	IMR90	lung:	n/a	n/a
7	YY1	chr2:38829344-38830866	GM12878	blood:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
8	SIN3AK20	chr2:38828533-38831144	MCF-7	breast:	n/a	n/a
9	CHD2	chr2:38829207-38830825	Hela-S3	cervix:	n/a	n/a
10	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
11	TAF1	chr2:38829302-38830510	K562	blood:	n/a	n/a
12	ZBTB7A	chr2:38828985-38830833	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr2:38828985-38830918	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr2:38829066-38830968	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr2:38829243-38830369	HL-60	blood:	n/a	n/a
16	CTCF	chr2:38829340-38829490	Caco-2	colon:	n/a	n/a
17	SMC3	chr2:38829250-38829396	Hela-S3	cervix:	n/a	n/a
18	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
19	TCF12	chr2:38828537-38831166	A549	lung:	n/a	n/a
20	RAD21	chr2:38827547-38831481	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr2:38829316-38830677	Hela-S3	cervix:	n/a	n/a
22	HEY1	chr2:38829004-38830548	K562	blood:	n/a	chr2:38829898-38829913 chr2:38830197-38830212
23	MAX	chr2:38829039-38831033	HepG2	liver:	n/a	n/a
24	CCNT2	chr2:38829100-38830931	K562	blood:	n/a	n/a
25	TAF1	chr2:38829374-38830551	A549	lung:	n/a	n/a
26	HEY1	chr2:38828474-38830907	HepG2	liver:	n/a	chr2:38829898-38829913 chr2:38830197-38830212
27	POLR2A	chr2:38829371-38830785	HepG2	liver:	n/a	n/a
28	POLR2A	chr2:38828579-38830561	K562	blood:	n/a	n/a
29	MAX	chr2:38829209-38831045	A549	lung:	n/a	n/a
30	YY1	chr2:38829156-38830520	K562	blood:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
31	YY1	chr2:38829291-38830197	K562	blood:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
32	GATA3	chr2:38829361-38831106	A549	lung:	n/a	n/a
33	SPI1	chr2:38829204-38830491	HL-60	blood:	n/a	chr2:38830015-38830028
34	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
35	YY1	chr2:38829313-38830906	GM12892	blood:	n/a	chr2:38829900-38829914 chr2:38830141-38830150 chr2:38829769-38829778 chr2:38829553-38829567 chr2:38829885-38829899
36	POLR2A	chr2:38829007-38830825	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr2:38829344-38830432	ProgFib	skin:	n/a	n/a
38	TAF1	chr2:38829291-38830533	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr2:38829326-38829490	SK-N-SH	brain:	n/a	n/a
40	REST	chr2:38828498-38831160	H1-neurons	neurons:	n/a	chr2:38830014-38830027 chr2:38829373-38829386 chr2:38830026-38830039 chr2:38829806-38829819
41	ZNF263	chr2:38829152-38830968	HEK293-T-REx	kidney:	n/a	chr2:38830099-38830108 chr2:38830012-38830033 chr2:38830020-38830029 chr2:38830023-38830032
42	MAX	chr2:38829313-38830907	MCF-7	breast:	n/a	n/a
43	TAF1	chr2:38829395-38830864	ECC-1	luminal epithelium:	n/a	n/a
44	CTCF	chr2:38829160-38831342	SK-N-SH	brain:	n/a	chr2:38830289-38830302 chr2:38830180-38830193
45	GABPA	chr2:38829064-38830467	K562	blood:	n/a	n/a
46	POLR2A	chr2:38829007-38830995	HL-60	blood:	n/a	n/a
47	CREB1	chr2:38829215-38829655	A549	lung:	n/a	n/a
48	MAX	chr2:38829278-38830929	K562	blood:	n/a	n/a
49	SIN3A	chr2:38828520-38831200	H1-hESC	embryonic stem cell:	n/a	chr2:38830115-38830126 chr2:38829851-38829864
50	REST	chr2:38829270-38830986	A549	lung:	n/a	chr2:38830014-38830027 chr2:38829373-38829386 chr2:38830026-38830039 chr2:38829806-38829819

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

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

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10495880	0.82[ASN][1000 genomes]
rs12105827	0.88[EUR][1000 genomes]
rs12987111	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12990659	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12995222	0.87[ASN][1000 genomes]
rs12996029	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13011896	0.96[AFR][1000 genomes]
rs1540436	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17421399	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17421503	0.83[AFR][1000 genomes]
rs17421743	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17493321	0.88[EUR][1000 genomes]
rs17493419	0.83[AFR][1000 genomes]
rs17493538	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17493573	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17493594	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864828	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864829	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1864830	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3213851	0.94[ASN][1000 genomes]
rs34218951	0.87[EUR][1000 genomes]
rs34462852	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35679136	0.88[AFR][1000 genomes]
rs35734673	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35933789	0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4268910	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56217714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544170	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6721860	0.80[EUR][1000 genomes]
rs6757844	0.84[EUR][1000 genomes]
rs68109027	0.81[AFR][1000 genomes]
rs72905846	0.81[AFR][1000 genomes]
rs72905865	0.82[ASN][1000 genomes]
rs72907903	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7573095	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7574556	0.88[EUR][1000 genomes]
rs934394	0.83[AFR][1000 genomes]
rs934395	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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