Variant report

Variant	rs6675408
Chromosome Location	chr1:227505713-227505714
allele	A/C
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	chr1:227505289-227507173	ProgFib	skin:	n/a	n/a
2	MAX	chr1:227505325-227505721	A549	lung:	n/a	chr1:227505659-227505669
3	YY1	chr1:227505680-227506782	K562	blood:	n/a	chr1:227506189-227506199 chr1:227506496-227506510 chr1:227506456-227506470 chr1:227505900-227505911 chr1:227506042-227506053 chr1:227505902-227505916 chr1:227505852-227505861 chr1:227505902-227505911 chr1:227506184-227506200 chr1:227505905-227505914 chr1:227505905-227505919 chr1:227506177-227506199 chr1:227506403-227506417
4	POLR2A	chr1:227505698-227507213	U87	brain:	n/a	n/a
5	CCNT2	chr1:227505228-227506682	K562	blood:	n/a	chr1:227506372-227506381
6	TAF1	chr1:227505586-227506708	K562	blood:	n/a	n/a
7	POLR2A	chr1:227505368-227507144	K562	blood:	n/a	n/a
8	HEY1	chr1:227505309-227507056	K562	blood:	n/a	chr1:227505900-227505915 chr1:227505654-227505669 chr1:227506721-227506736 chr1:227506549-227506564 chr1:227505897-227505912 chr1:227505819-227505834
9	ELF1	chr1:227505677-227506627	K562	blood:	n/a	chr1:227506013-227506022 chr1:227505902-227505911 chr1:227505697-227505709 chr1:227505897-227505909 chr1:227506497-227506509 chr1:227506509-227506521
10	POLR2A	chr1:227504780-227506688	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:227505416-227507157	GM19193	blood:	n/a	n/a
12	HA-E2F1	chr1:227505284-227506944	MCF-7	breast:	n/a	chr1:227505900-227505910 chr1:227505905-227505914 chr1:227505653-227505662 chr1:227505461-227505468 chr1:227505461-227505468 chr1:227505461-227505468
13	SIN3A	chr1:227504748-227507247	H1-hESC	embryonic stem cell:	n/a	chr1:227505012-227505021 chr1:227506503-227506512
14	ZBTB7A	chr1:227505329-227506982	K562	blood:	n/a	chr1:227505472-227505481 chr1:227505745-227505756 chr1:227506007-227506016 chr1:227505746-227505757
15	POLR2A	chr1:227504718-227507432	MCF10A-Er-Src	breast:	n/a	n/a
16	TAF1	chr1:227505277-227507245	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr1:227504749-227505748	Hela-S3	cervix:	n/a	chr1:227505313-227505322 chr1:227505659-227505669
18	CEBPB	chr1:227503465-227506205	Hela-S3	cervix:	n/a	chr1:227505283-227505294
19	TAF1	chr1:227505293-227507153	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:227505680-227507213	U87	brain:	n/a	n/a
21	SMARCB1	chr1:227505319-227506806	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:227505363-227507068	PBDE	blood:	n/a	n/a
23	MAX	chr1:227505249-227505728	SK-N-SH	brain:	n/a	chr1:227505313-227505322 chr1:227505659-227505669
24	CTCF	chr1:227505580-227505730	Hela-S3	cervix:	n/a	n/a
25	YY1	chr1:227505158-227506886	SK-N-SH	brain:	n/a	chr1:227506189-227506199 chr1:227506496-227506510 chr1:227506456-227506470 chr1:227505900-227505911 chr1:227506042-227506053 chr1:227505902-227505916 chr1:227505852-227505861 chr1:227505653-227505667 chr1:227505653-227505662 chr1:227505902-227505911 chr1:227506184-227506200 chr1:227505905-227505914 chr1:227505905-227505919 chr1:227506177-227506199 chr1:227506403-227506417
26	POLR2A	chr1:227505179-227506891	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr1:227505265-227507104	K562	blood:	n/a	n/a
28	POLR2A	chr1:227505589-227506727	A549	lung:	n/a	n/a
29	POLR2A	chr1:227505360-227506559	Hela-S3	cervix:	n/a	n/a
30	MAX	chr1:227505308-227507250	K562	blood:	n/a	chr1:227505850-227505860 chr1:227505313-227505322 chr1:227505659-227505669
31	YY1	chr1:227505711-227506588	K562	blood:	n/a	chr1:227506189-227506199 chr1:227506496-227506510 chr1:227506456-227506470 chr1:227505900-227505911 chr1:227506042-227506053 chr1:227505902-227505916 chr1:227505852-227505861 chr1:227505902-227505911 chr1:227506184-227506200 chr1:227505905-227505914 chr1:227505905-227505919 chr1:227506177-227506199 chr1:227506403-227506417
32	POLR2A	chr1:227503661-227507169	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr1:227505234-227506726	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr1:227505136-227507250	H1-neurons	neurons:	n/a	n/a
35	CHD2	chr1:227505246-227506367	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:227505180-227507349	H1-hESC	embryonic stem cell:	n/a	n/a
37	REST	chr1:227505691-227506636	K562	blood:	n/a	chr1:227505931-227505949 chr1:227506502-227506512
38	ZNF263	chr1:227505318-227507155	HEK293-T-REx	kidney:	n/a	n/a
39	POLR2A	chr1:227505607-227505823	A549	lung:	n/a	n/a
40	POLR2A	chr1:227505188-227505753	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr1:227505293-227507055	K562	blood:	n/a	n/a
42	UBTF	chr1:227504410-227507285	K562	blood:	n/a	n/a
43	POLR2A	chr1:227505161-227507261	SK-N-MC	brain:	n/a	n/a
44	TAF1	chr1:227505233-227506697	K562	blood:	n/a	n/a
45	POLR2A	chr1:227505685-227507097	A549	lung:	n/a	n/a
46	POLR2A	chr1:227505306-227507267	MCF-7	breast:	n/a	n/a
47	TCF7L2	chr1:227505660-227506642	HCT-116	colon:	n/a	chr1:227505874-227505881
48	ZMIZ1	chr1:227505322-227507058	K562	blood:	n/a	n/a
49	MYC	chr1:227504812-227507164	K562	blood:	n/a	chr1:227505850-227505860 chr1:227505313-227505322 chr1:227505659-227505669
50	POLR2A	chr1:227503727-227507111	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227365298..227367002-chr1:227505047..227506997,2	K562	blood:
2	chr1:227505566..227506340-chr10:95653162..95653749,2	HCT-116	colon:
3	chr1:227125150..227128196-chr1:227505421..227508280,4	MCF-7	breast:
4	chr1:227126362..227128612-chr1:227504788..227507568,2	MCF-7	breast:
5	chr1:227505582..227506201-chr3:119217404..119218268,2	Hela-S3	cervix:
6	chr1:227505349..227507259-chr17:61552926..61555906,2	MCF-7	breast:
7	chr1:227500962..227504758-chr1:227504964..227507747,3	MCF-7	breast:
8	chr1:227504778..227506670-chr1:227579538..227582289,3	K562	blood:
9	chr1:227504042..227507688-chr1:227616722..227620233,4	K562	blood:
10	chr1:227505544..227508414-chr1:227579779..227582450,2	MCF-7	breast:
11	chr1:227505302..227507077-chr1:227617949..227620450,2	MCF-7	breast:
12	chr1:227505645..227506241-chr4:122791074..122791739,2	Hela-S3	cervix:
13	chr1:227504778..227506536-chr1:227579859..227582289,2	K562	blood:

Variant related genes	Relation type
CDC42BPA	TF binding region
ENSG00000159640	Chromatin interaction
ENSG00000261501	Chromatin interaction
ENSG00000176273	Chromatin interaction
ENSG00000163050	Chromatin interaction
ENSG00000143776	Chromatin interaction
ENSG00000234277	Chromatin interaction
ENSG00000242757	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000138686	Chromatin interaction
ENSG00000228625	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10916116	0.83[ASN][1000 genomes]
rs10916125	0.81[AMR][1000 genomes]
rs12119153	0.83[ASN][1000 genomes]
rs12131933	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138092	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12746316	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34113967	0.97[ASN][1000 genomes]
rs61834323	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61834324	0.97[ASN][1000 genomes]
rs61834326	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6697583	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518813	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7523759	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539662	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7548118	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv3390376	chr1:227505104-227507452	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227500800-227506600	Active TSS	K562	blood
2	chr1:227501400-227506800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:227501400-227507000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:227501600-227507000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:227501800-227505800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:227501800-227506600	Active TSS	Fetal Stomach	stomach
7	chr1:227501800-227506600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:227501800-227506600	Active TSS	HMEC	breast
9	chr1:227501800-227506600	Active TSS	NHEK	skin
10	chr1:227501800-227506800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:227501800-227506800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:227501800-227506800	Active TSS	Brain Anterior Caudate	brain
13	chr1:227501800-227506800	Active TSS	A549	lung
14	chr1:227501800-227506800	Active TSS	NHLF	lung
15	chr1:227501800-227507000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:227501800-227507000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr1:227501800-227507000	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr1:227501800-227507000	Active TSS	Fetal Kidney	kidney
19	chr1:227501800-227507200	Active TSS	Duodenum Mucosa	Duodenum
20	chr1:227501800-227507200	Active TSS	NHDF-Ad	bronchial
21	chr1:227502000-227506600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:227502000-227506600	Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:227502000-227506600	Active TSS	Colonic Mucosa	Colon
24	chr1:227502000-227506600	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr1:227502000-227506600	Active TSS	HUVEC	blood vessel
26	chr1:227502000-227506800	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr1:227502000-227506800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:227502000-227506800	Active TSS	Stomach Smooth Muscle	stomach
29	chr1:227502000-227506800	Active TSS	NH-A	brain
30	chr1:227502000-227507000	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:227502000-227507000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr1:227502000-227507000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:227502000-227507000	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr1:227502000-227507000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:227502000-227507000	Active TSS	Brain Angular Gyrus	brain
36	chr1:227502000-227507000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:227502000-227507000	Active TSS	Brain Substantia Nigra	brain
38	chr1:227502000-227507000	Active TSS	HSMMtube	muscle
39	chr1:227502000-227507200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:227502000-227507200	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr1:227502000-227507200	Active TSS	Psoas Muscle	Psoas
42	chr1:227502200-227506800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:227502200-227506800	Active TSS	Brain Cingulate Gyrus	brain
44	chr1:227502200-227506800	Active TSS	Fetal Muscle Leg	muscle
45	chr1:227502200-227507000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:227502200-227507200	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr1:227502200-227507600	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr1:227502400-227507000	Active TSS	H1 Cell Line	embryonic stem cell
49	chr1:227502600-227506600	Active TSS	HSMM	muscle
50	chr1:227502600-227506800	Active TSS	Brain Hippocampus Middle	brain

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