Variant report

Variant	rs11577976
Chromosome Location	chr1:228333652-228333653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF1	chr1:228333337-228333707	K562	blood:	n/a	n/a
2	POLR2A	chr1:228332924-228334939	K562	blood:	n/a	n/a
3	CEBPB	chr1:228333267-228333694	K562	blood:	n/a	n/a
4	TEAD4	chr1:228333129-228333774	K562	blood:	n/a	n/a
5	STAT5A	chr1:228333216-228333732	K562	blood:	n/a	n/a
6	RCOR1	chr1:228333074-228333839	K562	blood:	n/a	n/a
7	GATA2	chr1:228333261-228333739	K562	blood:	n/a	n/a
8	POLR2A	chr1:228333210-228333746	K562	blood:	n/a	n/a
9	REST	chr1:228333339-228333677	K562	blood:	n/a	n/a
10	TBL1XR1	chr1:228333250-228333739	K562	blood:	n/a	n/a
11	TEAD4	chr1:228333149-228333798	K562	blood:	n/a	n/a
12	MYC	chr1:228333331-228333760	K562	blood:	n/a	n/a
13	ZMIZ1	chr1:228333292-228333767	K562	blood:	n/a	n/a
14	POLR2A	chr1:228332644-228338827	K562	blood:	n/a	n/a
15	CBX3	chr1:228333045-228333801	K562	blood:	n/a	n/a
16	UBTF	chr1:228333163-228333732	K562	blood:	n/a	n/a
17	POLR2A	chr1:228332372-228333985	K562	blood:	n/a	n/a
18	HCFC1	chr1:228333405-228333673	K562	blood:	n/a	n/a
19	YY1	chr1:228333360-228333690	K562	blood:	n/a	n/a
20	JUND	chr1:228333184-228333707	K562	blood:	n/a	n/a
21	POLR2A	chr1:228333353-228333710	Hela-S3	cervix:	n/a	n/a
22	MYC	chr1:228333301-228333738	K562	blood:	n/a	n/a
23	EGR1	chr1:228333355-228333666	K562	blood:	n/a	n/a
24	ETS1	chr1:228333340-228333791	K562	blood:	n/a	n/a
25	GATA1	chr1:228333334-228333672	PBDEFetal	blood:	n/a	n/a
26	GABPA	chr1:228333293-228333761	K562	blood:	n/a	n/a
27	YY1	chr1:228333274-228333716	K562	blood:	n/a	n/a
28	POLR2A	chr1:228333255-228333763	K562	blood:	n/a	n/a
29	E2F6	chr1:228333535-228333710	K562	blood:	n/a	n/a
30	CCNT2	chr1:228333173-228333982	K562	blood:	n/a	n/a
31	NR2F2	chr1:228332706-228334135	K562	blood:	n/a	n/a
32	NR2F2	chr1:228333226-228333744	K562	blood:	n/a	n/a
33	GABPA	chr1:228333340-228333741	K562	blood:	n/a	n/a
34	POLR2A	chr1:228331544-228333910	K562	blood:	n/a	n/a
35	ARID3A	chr1:228333364-228333655	K562	blood:	n/a	n/a
36	STAT5A	chr1:228333279-228333662	K562	blood:	n/a	n/a
37	POLR2A	chr1:228333073-228335536	GM12878	blood:	n/a	n/a
38	GATA1	chr1:228333304-228333842	K562	blood:	n/a	n/a
39	HDAC2	chr1:228333293-228333696	K562	blood:	n/a	n/a
40	RCOR1	chr1:228333165-228333753	K562	blood:	n/a	n/a
41	PML	chr1:228333273-228333709	K562	blood:	n/a	n/a
42	CEBPD	chr1:228333204-228333795	K562	blood:	n/a	n/a
43	GATA2	chr1:228333278-228333671	K562	blood:	n/a	n/a
44	GATA1	chr1:228333061-228334105	PBDE	blood:	n/a	n/a
45	ZBTB7A	chr1:228333224-228333847	K562	blood:	n/a	n/a
46	GATA2	chr1:228333235-228333905	K562	blood:	n/a	n/a
47	TBL1XR1	chr1:228333256-228333710	K562	blood:	n/a	n/a
48	MAX	chr1:228332853-228333978	K562	blood:	n/a	n/a
49	POLR2A	chr1:228333547-228333655	Hela-S3	cervix:	n/a	n/a
50	ZNF143	chr1:228333090-228333729	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228289389..228292049-chr1:228333496..228335357,2	K562	blood:
2	chr1:228284520..228292111-chr1:228324853..228335412,14	K562	blood:

No data

Variant related genes	Relation type
GJC2	TF binding region
GUK1	TF binding region
ENSG00000143793	Chromatin interaction
ENSG00000264944	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10127705	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1048503	1.00[ASW][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.84[LWK][hapmap]
rs10495278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495279	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916262	1.00[ASW][hapmap]
rs10916266	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1094602	1.00[EUR][1000 genomes]
rs1094603	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11580599	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11581037	1.00[CEU][hapmap]
rs11581169	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582369	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11584418	1.00[CEU][hapmap]
rs11584499	1.00[ASW][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap]
rs11586055	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs11589513	1.00[ASW][hapmap]
rs12034268	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12039801	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12088423	1.00[CEU][hapmap]
rs1771486	0.85[EUR][1000 genomes]
rs1803695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28587961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34687764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738680	1.00[ASW][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.84[LWK][hapmap]
rs3738681	1.00[ASW][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.84[LWK][hapmap]
rs3795773	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3795774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41303083	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653906	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs4653908	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653909	0.90[EUR][1000 genomes]
rs4653914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61825156	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61825157	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825159	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61827462	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6663726	0.90[EUR][1000 genomes]
rs6668719	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs7530253	1.00[EUR][1000 genomes]
rs7537552	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs882451	1.00[ASW][hapmap]
rs9287011	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9970544	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS 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 miRNA target site	133 gene(s)	inside rSNPs	diseases
8	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised 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 miRNA target site	106 gene(s)	inside rSNPs	diseases
9	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
10	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
11	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS 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	64 gene(s)	inside rSNPs	diseases
12	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
13	nsv549290	chr1:228333652-228349806	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228329000-228336800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:228329000-228339400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:228329000-228339600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:228329200-228337400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:228329400-228333800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:228329400-228333800	Genic enhancers	Spleen	Spleen
7	chr1:228329400-228336600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:228329400-228337600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:228329400-228337600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:228329400-228338200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:228329600-228335200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:228329600-228335600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:228329600-228336800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:228329800-228336400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:228329800-228336600	Weak transcription	A549	lung
16	chr1:228330000-228334800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:228330000-228335800	Weak transcription	Fetal Lung	lung
18	chr1:228330000-228337200	Genic enhancers	Fetal Muscle Leg	muscle
19	chr1:228330000-228337800	Genic enhancers	Lung	lung
20	chr1:228330200-228336200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:228330600-228337200	Genic enhancers	Fetal Muscle Trunk	muscle
22	chr1:228331000-228335600	Weak transcription	HUVEC	blood vessel
23	chr1:228331000-228335800	Strong transcription	Fetal Stomach	stomach
24	chr1:228331000-228338800	Weak transcription	HSMMtube	muscle
25	chr1:228331200-228333800	Genic enhancers	Thymus	Thymus
26	chr1:228331200-228336000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:228331400-228341800	Weak transcription	Psoas Muscle	Psoas
28	chr1:228331600-228337000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:228331600-228337000	Weak transcription	NH-A	brain
30	chr1:228331600-228341000	Genic enhancers	Fetal Thymus	thymus
31	chr1:228331800-228335800	Weak transcription	Brain Substantia Nigra	brain
32	chr1:228331800-228336400	Weak transcription	NHDF-Ad	bronchial
33	chr1:228331800-228336600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:228331800-228336800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:228332000-228334600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:228332000-228335800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:228332000-228336200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:228332000-228336400	Weak transcription	Hela-S3	cervix
39	chr1:228332000-228336400	Weak transcription	HSMM	muscle
40	chr1:228332000-228336600	Weak transcription	Fetal Heart	heart
41	chr1:228332000-228337000	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr1:228332200-228333800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:228332200-228334400	Weak transcription	HMEC	breast
44	chr1:228332200-228334800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:228332200-228334800	Weak transcription	Brain Angular Gyrus	brain
46	chr1:228332200-228335600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:228332200-228335800	Weak transcription	Right Atrium	heart
48	chr1:228332200-228336000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:228332200-228336200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:228332200-228337400	Strong transcription	Dnd41	blood

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