Variant report

Variant	rs6672433
Chromosome Location	chr1:226250927-226250928
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	chr1:226249047-226251609	Hela-S3	cervix:	n/a	n/a
2	CHD1	chr1:226248795-226252344	IMR90	lung:	n/a	chr1:226250205-226250215 chr1:226250686-226250696 chr1:226250156-226250166 chr1:226250759-226250769 chr1:226250029-226250039
3	POLR2A	chr1:226249356-226251735	GM18505	blood:	n/a	n/a
4	POLR2A	chr1:226249375-226251078	ECC-1	luminal epithelium:	n/a	n/a
5	TAF1	chr1:226250304-226251627	H1-neurons	neurons:	n/a	n/a
6	CTCF	chr1:226250800-226250950	RPTEC	kidney:	n/a	n/a
7	MXI1	chr1:226248834-226251514	Hela-S3	cervix:	n/a	n/a
8	TAF7	chr1:226249366-226252248	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr1:226249133-226251486	SK-N-SH	brain:	n/a	chr1:226249735-226249749 chr1:226249769-226249780 chr1:226250437-226250446 chr1:226250796-226250807 chr1:226250432-226250446 chr1:226250678-226250692 chr1:226249556-226249575 chr1:226249558-226249580 chr1:226250013-226250022 chr1:226249561-226249569 chr1:226250412-226250420 chr1:226250442-226250451 chr1:226250678-226250687 chr1:226250799-226250808 chr1:226250972-226250984
10	YY1	chr1:226250224-226251430	A549	lung:	n/a	chr1:226250437-226250446 chr1:226250796-226250807 chr1:226250432-226250446 chr1:226250678-226250692 chr1:226250412-226250420 chr1:226250442-226250451 chr1:226250678-226250687 chr1:226250799-226250808 chr1:226250972-226250984
11	SIN3AK20	chr1:226250813-226251078	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr1:226249337-226251503	NB4	blood:	n/a	n/a
13	POLR2A	chr1:226250287-226251012	GM12878	blood:	n/a	n/a
14	ZNF263	chr1:226250324-226252300	HEK293-T-REx	kidney:	n/a	chr1:226250755-226250764 chr1:226250752-226250761
15	SIN3AK20	chr1:226249467-226251625	K562	blood:	n/a	n/a
16	PML	chr1:226249030-226251155	K562	blood:	n/a	n/a
17	POLR2A	chr1:226249112-226251663	HUVEC	blood vessel:	n/a	n/a
18	MAX	chr1:226249258-226251649	K562	blood:	n/a	chr1:226251147-226251156 chr1:226251147-226251156 chr1:226251146-226251157 chr1:226251148-226251155
19	POLR2A	chr1:226248810-226256763	K562	blood:	n/a	n/a
20	YY1	chr1:226250772-226251556	SK-N-SH_RA	brain:	n/a	chr1:226250796-226250807 chr1:226250799-226250808 chr1:226250972-226250984
21	POLR2A	chr1:226250302-226252891	PBDE	blood:	n/a	n/a
22	POLR2A	chr1:226250912-226250965	Gliobla	brain:	n/a	n/a
23	YY1	chr1:226249298-226251372	HepG2	liver:	n/a	chr1:226249735-226249749 chr1:226249769-226249780 chr1:226250437-226250446 chr1:226250796-226250807 chr1:226250432-226250446 chr1:226250678-226250692 chr1:226249556-226249575 chr1:226249558-226249580 chr1:226250013-226250022 chr1:226249561-226249569 chr1:226250412-226250420 chr1:226250442-226250451 chr1:226250678-226250687 chr1:226250799-226250808 chr1:226250972-226250984
24	POLR2A	chr1:226249406-226250965	K562	blood:	n/a	n/a
25	TBP	chr1:226250874-226251567	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:226249126-226251671	K562	blood:	n/a	n/a
27	POLR2A	chr1:226250816-226251328	GM12891	blood:	n/a	n/a
28	TCF7L2	chr1:226249398-226250952	HCT-116	colon:	n/a	n/a
29	TBL1XR1	chr1:226250919-226252972	K562	blood:	n/a	n/a
30	YY1	chr1:226249326-226251539	GM12878	blood:	n/a	chr1:226249735-226249749 chr1:226249769-226249780 chr1:226250437-226250446 chr1:226250796-226250807 chr1:226250432-226250446 chr1:226250678-226250692 chr1:226249556-226249575 chr1:226249558-226249580 chr1:226250013-226250022 chr1:226249561-226249569 chr1:226250412-226250420 chr1:226250442-226250451 chr1:226250678-226250687 chr1:226250799-226250808 chr1:226250972-226250984
31	YY1	chr1:226250691-226251236	GM12892	blood:	n/a	chr1:226250796-226250807 chr1:226250799-226250808 chr1:226250972-226250984
32	RELA	chr1:226250373-226251568	GM10847	blood:	n/a	n/a
33	CTCF	chr1:226249723-226253106	SK-N-SH	brain:	n/a	chr1:226252680-226252698 chr1:226250667-226250685 chr1:226252682-226252703
34	POLR2A	chr1:226249055-226251570	K562	blood:	n/a	n/a
35	YY1	chr1:226249309-226251367	GM12891	blood:	n/a	chr1:226249735-226249749 chr1:226249769-226249780 chr1:226250437-226250446 chr1:226250796-226250807 chr1:226250432-226250446 chr1:226250678-226250692 chr1:226249556-226249575 chr1:226249558-226249580 chr1:226250013-226250022 chr1:226249561-226249569 chr1:226250412-226250420 chr1:226250442-226250451 chr1:226250678-226250687 chr1:226250799-226250808 chr1:226250972-226250984
36	ELF1	chr1:226249385-226250981	GM12878	blood:	n/a	chr1:226250583-226250595 chr1:226250013-226250022 chr1:226250678-226250687 chr1:226250437-226250446
37	POLR2A	chr1:226250313-226251031	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr1:226250306-226251198	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr1:226249438-226252304	K562	blood:	n/a	n/a
40	POLR2A	chr1:226249363-226251573	GM12892	blood:	n/a	n/a
41	POLR2A	chr1:226249009-226251573	HL-60	blood:	n/a	n/a
42	TEAD4	chr1:226250284-226252350	K562	blood:	n/a	chr1:226251700-226251709
43	RELA	chr1:226250306-226251610	GM12891	blood:	n/a	n/a
44	POLR2A	chr1:226250806-226251020	GM12891	blood:	n/a	n/a
45	POLR2A	chr1:226250091-226251462	U87	brain:	n/a	n/a
46	POLR2A	chr1:226249356-226251543	HUVEC	blood vessel:	n/a	n/a
47	CTCF	chr1:226250281-226250931	K562	blood:	n/a	chr1:226250667-226250685
48	EGR1	chr1:226249619-226251024	K562	blood:	n/a	chr1:226249990-226250000 chr1:226250856-226250870 chr1:226250011-226250024 chr1:226250116-226250130
49	SIN3A	chr1:226249154-226252868	H1-hESC	embryonic stem cell:	n/a	chr1:226250460-226250473 chr1:226249897-226249908
50	POLR2A	chr1:226249403-226251047	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226053730..226055639-chr1:226248303..226251048,2	MCF-7	breast:
2	chr1:226183087..226192322-chr1:226243551..226254243,95	K562	blood:
3	chr1:226247680..226258196-chr1:226306136..226315725,36	MCF-7	breast:
4	chr1:225964211..225968767-chr1:226248453..226252378,4	K562	blood:
5	chr1:226183029..226192481-chr1:226247725..226253108,31	MCF-7	breast:
6	chr1:226184876..226191468-chr1:226247585..226254254,12	MCF-7	breast:
7	chr1:226249145..226251355-chr5:138634621..138637026,2	MCF-7	breast:
8	chr1:226249721..226252045-chr1:226495735..226498532,3	K562	blood:
9	chr1:226250436..226250975-chr3:171528336..171529225,2	Hela-S3	cervix:
10	chr1:226186794..226187828-chr1:226250346..226251520,3	NB4	blood:
11	chr1:225614646..225616665-chr1:226249352..226251446,2	K562	blood:
12	chr1:225839962..225842492-chr1:226249684..226252539,2	MCF-7	breast:
13	chr1:45284133..45286762-chr1:226249402..226251655,2	K562	blood:
14	chr1:226250042..226250975-chr7:123197373..123197919,2	Hela-S3	cervix:
15	chr1:225838732..225840997-chr1:226248323..226251215,2	MCF-7	breast:
16	chr1:226248851..226254336-chr1:226269112..226274282,12	MCF-7	breast:
17	chr1:226248789..226253333-chr1:226269675..226273948,8	MCF-7	breast:
18	chr1:226250265..226250927-chr4:99916726..99917637,2	HCT-116	colon:
19	chr1:226247784..226253760-chr1:226305545..226317702,29	MCF-7	breast:
20	chr1:226178791..226193771-chr1:226246813..226256535,111	K562	blood:

Variant related genes	Relation type
H3F3A	TF binding region
ENSG00000272562	TF binding region
ENSG00000143815	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000270598	Chromatin interaction
ENSG00000225518	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000128609	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000199545	Chromatin interaction
ENSG00000154380	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000183814	Chromatin interaction
ENSG00000075651	Chromatin interaction
ENSG00000143751	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16845569	0.80[AFR][1000 genomes]
rs16845579	0.80[AFR][1000 genomes]
rs73083508	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73083551	0.83[AFR][1000 genomes]
rs73100540	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	esv3327023	chr1:226248854-226251702	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	n/a
4	esv3386707	chr1:226249329-226251427	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226248200-226253400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr1:226248800-226252600	Active TSS	NH-A	brain
3	chr1:226248800-226252800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:226248800-226252800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:226248800-226253000	Active TSS	NHLF	lung
6	chr1:226248800-226253200	Active TSS	Colonic Mucosa	Colon
7	chr1:226248800-226253400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr1:226248800-226253400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:226249000-226252400	Active TSS	HSMM	muscle
10	chr1:226249000-226252600	Active TSS	Colon Smooth Muscle	Colon
11	chr1:226249000-226252600	Active TSS	Fetal Brain Female	brain
12	chr1:226249000-226252800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:226249000-226252800	Active TSS	Left Ventricle	heart
14	chr1:226249000-226253000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:226249000-226253000	Active TSS	Psoas Muscle	Psoas
16	chr1:226249000-226253200	Active TSS	Fetal Muscle Trunk	muscle
17	chr1:226249000-226253200	Active TSS	Ovary	ovary
18	chr1:226249000-226253400	Active TSS	Fetal Intestine Large	intestine
19	chr1:226249000-226253400	Active TSS	Right Ventricle	heart
20	chr1:226249200-226252000	Active TSS	Small Intestine	intestine
21	chr1:226249200-226252200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:226249200-226252200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:226249200-226252200	Active TSS	Esophagus	oesophagus
24	chr1:226249200-226252200	Active TSS	Lung	lung
25	chr1:226249200-226252200	Active TSS	Pancreas	Pancrea
26	chr1:226249200-226252400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:226249200-226252400	Active TSS	Brain Anterior Caudate	brain
28	chr1:226249200-226252400	Active TSS	Placenta Amnion	Placenta Amnion
29	chr1:226249200-226252600	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr1:226249200-226252800	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr1:226249200-226252800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:226249200-226252800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:226249200-226252800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:226249200-226252800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:226249200-226252800	Active TSS	Brain Germinal Matrix	brain
36	chr1:226249200-226253000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:226249200-226253000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:226249200-226253000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:226249200-226253000	Active TSS	Aorta	Aorta
40	chr1:226249200-226253400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:226249200-226253400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:226249200-226253400	Active TSS	Fetal Intestine Small	intestine
43	chr1:226249400-226251400	Transcr. at gene 5' and 3'	Right Atrium	heart
44	chr1:226249400-226251800	Active TSS	Gastric	stomach
45	chr1:226249400-226252000	Active TSS	Rectal Smooth Muscle	rectum
46	chr1:226249400-226252200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:226249400-226252200	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:226249400-226252200	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr1:226249400-226252200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:226249400-226252200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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