Variant report

Variant	rs6426507
Chromosome Location	chr1:228782786-228782787
allele	A/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	CTCF	chr1:228782780-228782930	HPAF	blood vessel:	n/a	n/a
2	CTCF	chr1:228782755-228782843	NHEK	skin:	n/a	n/a
3	POLR2A	chr1:228782399-228784218	Hela-S3	cervix:	n/a	n/a
4	JUND	chr1:228776890-228782900	A549	lung:	n/a	chr1:228780091-228780105 chr1:228777850-228777864 chr1:228782322-228782336 chr1:228781259-228781268 chr1:228779028-228779037
5	CTCF	chr1:228782680-228782830	HCPEpiC	choroid plexus:	n/a	n/a
6	MYC	chr1:228782471-228782922	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr1:228782640-228782790	GM06990	blood:	n/a	n/a
8	CTCF	chr1:228782680-228782830	GM12874	blood:	n/a	n/a
9	WRNIP1	chr1:228782747-228782845	GM12878	blood:	n/a	n/a
10	SMARCB1	chr1:228782483-228784310	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:228782420-228783936	HepG2	liver:	n/a	n/a
12	CTCF	chr1:228782760-228782910	GM12871	blood:	n/a	n/a
13	GABPA	chr1:228782573-228782898	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr1:228782455-228784026	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr1:228782343-228784099	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr1:228782660-228782810	AG09319	gingival:	n/a	n/a
17	POLR2A	chr1:228782361-228784289	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:228782416-228784035	GM15510	blood:	n/a	n/a
19	POLR2A	chr1:228782354-228783551	NB4	blood:	n/a	n/a
20	POLR2A	chr1:228782415-228782839	A549	lung:	n/a	n/a
21	TBP	chr1:228782708-228783025	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr1:228782700-228782850	HCM	heart:	n/a	n/a
23	REST	chr1:228782549-228782908	A549	lung:	n/a	chr1:228782772-228782790
24	SIN3AK20	chr1:228782344-228782937	A549	lung:	n/a	n/a
25	CTCF	chr1:228782660-228782810	GM12864	blood:	n/a	n/a
26	MAZ	chr1:228782572-228783886	Hela-S3	cervix:	n/a	n/a
27	E2F6	chr1:228782547-228784030	A549	lung:	n/a	chr1:228783805-228783812 chr1:228783095-228783105 chr1:228783096-228783107 chr1:228783096-228783104 chr1:228783095-228783106 chr1:228783943-228783952 chr1:228783084-228783098 chr1:228783096-228783103 chr1:228783384-228783396 chr1:228783096-228783104
28	CTCF	chr1:228782700-228782850	AG04450	lung:	n/a	n/a
29	CTCF	chr1:228782680-228782830	HPF	lung:	n/a	n/a
30	CHD2	chr1:228782398-228784265	Hela-S3	cervix:	n/a	chr1:228783099-228783109 chr1:228783311-228783321 chr1:228783805-228783812
31	CHD2	chr1:228782613-228782905	H1-hESC	embryonic stem cell:	n/a	n/a
32	TBP	chr1:228782430-228785001	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr1:228782434-228782977	H1-neurons	neurons:	n/a	n/a
34	RCOR1	chr1:228782490-228783979	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr1:228782755-228784050	A549	lung:	n/a	n/a
36	POLR2A	chr1:228782342-228784357	Hela-S3	cervix:	n/a	n/a
37	CTBP2	chr1:228782732-228784117	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr1:228782660-228782810	HPAF	blood vessel:	n/a	n/a
39	SP1	chr1:228781284-228784045	A549	lung:	n/a	chr1:228782216-228782226 chr1:228782343-228782353 chr1:228782780-228782794 chr1:228782216-228782226
40	REST	chr1:228782417-228783041	A549	lung:	n/a	chr1:228782772-228782790
41	POLR2A	chr1:228782775-228782954	A549	lung:	n/a	n/a
42	CTCF	chr1:228782740-228782890	AG09309	skin:	n/a	n/a
43	CTCF	chr1:228782660-228782810	SAEC	small airway:	n/a	n/a
44	MAX	chr1:228782411-228784428	A549	lung:	n/a	chr1:228784239-228784249
45	MYC	chr1:228782557-228782950	MCF10A-Er-Src	breast:	n/a	n/a
46	CTCF	chr1:228782741-228782829	HepG2	liver:	n/a	n/a
47	NRF1	chr1:228782419-228783042	SK-N-SH	brain:	n/a	n/a
48	CTCF	chr1:228782520-228782790	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr1:228782720-228782870	HBMEC	blood vessel:	n/a	n/a
50	ELK4	chr1:228782544-228783112	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228782241..228785119-chr1:228785249..228788137,2	K562	blood:

Variant related genes	Relation type
DUSP5P1	TF binding region
RNA5S16	TF binding region
RNA5S17	TF binding region
ENSG00000183929	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10753451	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10753452	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916338	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12028431	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12035708	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12140890	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12407568	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1925714	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1925717	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1925721	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1925722	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2182200	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35598069	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35724040	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147255	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4147256	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4412590	0.87[EUR][1000 genomes]
rs4653558	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653977	0.87[ASN][1000 genomes]
rs4653979	0.84[ASN][1000 genomes]
rs6426505	0.83[EUR][1000 genomes]
rs6670856	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs728964	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7415895	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs744668	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7533560	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv827075	chr1:228716554-228783674	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
4	nsv945355	chr1:228716611-228784016	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases
5	esv19715	chr1:228742638-228783674	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
6	esv3425415	chr1:228742829-228783527	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
7	nsv827086	chr1:228742962-228783035	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	nsv820567	chr1:228742962-228783403	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
9	nsv827097	chr1:228742962-228783403	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
10	esv3331974	chr1:228743029-228783527	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
11	esv3342484	chr1:228743029-228783527	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
12	esv3382956	chr1:228743029-228783527	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
13	esv3445359	chr1:228743029-228783527	Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
14	esv3450984	chr1:228743029-228783527	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
15	esv1831035	chr1:228758016-228782866	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
16	esv1828070	chr1:228758016-228793246	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 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	chr1:228782400-228782800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
2	chr1:228782400-228782800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:228782400-228782800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:228782400-228782800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:228782400-228782800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:228782400-228782800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:228782400-228782800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr1:228782400-228782800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:228782400-228782800	Active TSS	Muscle Satellite Cultured Cells	--
10	chr1:228782400-228782800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:228782400-228782800	Flanking Active TSS	Placenta	Placenta
12	chr1:228782400-228782800	Active TSS	Placenta Amnion	Placenta Amnion
13	chr1:228782400-228782800	Active TSS	HepG2	liver
14	chr1:228782400-228782800	Active TSS	HSMMtube	muscle
15	chr1:228782400-228783000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:228782400-228783000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:228782400-228783000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:228782400-228783000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:228782400-228783000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr1:228782400-228783000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
21	chr1:228782400-228783000	Flanking Active TSS	Colonic Mucosa	Colon
22	chr1:228782400-228783000	Flanking Active TSS	Lung	lung
23	chr1:228782400-228783000	Bivalent/Poised TSS	Thymus	Thymus
24	chr1:228782400-228783000	Enhancers	Spleen	Spleen
25	chr1:228782400-228783400	Flanking Bivalent TSS/Enh	Liver	Liver
26	chr1:228782400-228783800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:228782400-228783800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
28	chr1:228782400-228784000	Flanking Bivalent TSS/Enh	Dnd41	blood
29	chr1:228782400-228784200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:228782400-228784200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:228782400-228784200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
33	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
34	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
35	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
36	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
38	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
39	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
41	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
42	chr1:228782400-228784200	Flanking Active TSS	Pancreas	Pancrea
43	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
44	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
45	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
46	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
47	chr1:228782400-228784200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
48	chr1:228782400-228784400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
49	chr1:228782400-228784400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:228782400-228784400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

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