Variant report

Variant	rs35724040
Chromosome Location	chr1:228782519-228782520
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	POLR2A	chr1:228781306-228782710	PFSK-1	brain:	n/a	n/a
2	MAX	chr1:228782477-228782718	HepG2	liver:	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	chr1:228782500-228782650	AG04449	skin:	n/a	n/a
6	MYC	chr1:228782471-228782922	MCF10A-Er-Src	breast:	n/a	n/a
7	SMARCB1	chr1:228782483-228784310	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:228782420-228783936	HepG2	liver:	n/a	n/a
9	MAX	chr1:228782406-228782687	K562	blood:	n/a	n/a
10	MAX	chr1:228782455-228784026	ECC-1	luminal epithelium:	n/a	n/a
11	FOXP2	chr1:228782440-228782697	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr1:228782343-228784099	Hela-S3	cervix:	n/a	n/a
13	BHLHE40	chr1:228782486-228782780	HepG2	liver:	n/a	n/a
14	ELK1	chr1:228782519-228782770	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:228782361-228784289	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:228782416-228784035	GM15510	blood:	n/a	n/a
17	POLR2A	chr1:228782354-228783551	NB4	blood:	n/a	n/a
18	POLR2A	chr1:228782415-228782839	A549	lung:	n/a	n/a
19	SIN3AK20	chr1:228782344-228782937	A549	lung:	n/a	n/a
20	CHD2	chr1:228782398-228784265	Hela-S3	cervix:	n/a	chr1:228783099-228783109 chr1:228783311-228783321 chr1:228783805-228783812
21	E2F6	chr1:228782479-228782589	K562	blood:	n/a	n/a
22	TBP	chr1:228782430-228785001	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:228782434-228782977	H1-neurons	neurons:	n/a	n/a
24	POLR2A	chr1:228782446-228782602	A549	lung:	n/a	n/a
25	RCOR1	chr1:228782490-228783979	Hela-S3	cervix:	n/a	n/a
26	MAX	chr1:228782474-228782710	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:228782342-228784357	Hela-S3	cervix:	n/a	n/a
28	BHLHE40	chr1:228782373-228782758	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:228782505-228782563	ProgFib	skin:	n/a	n/a
30	SP1	chr1:228781284-228784045	A549	lung:	n/a	chr1:228782216-228782226 chr1:228782343-228782353 chr1:228782780-228782794 chr1:228782216-228782226
31	REST	chr1:228782417-228783041	A549	lung:	n/a	chr1:228782772-228782790
32	MAX	chr1:228782411-228784428	A549	lung:	n/a	chr1:228784239-228784249
33	NRF1	chr1:228782419-228783042	SK-N-SH	brain:	n/a	n/a
34	MAX	chr1:228782455-228782604	K562	blood:	n/a	n/a
35	POLR2A	chr1:228782377-228784212	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr1:228779071-228784168	PANC-1	pancreas:	n/a	n/a
37	ZNF143	chr1:228782486-228782817	Hela-S3	cervix:	n/a	n/a
38	BHLHE40	chr1:228782393-228782773	K562	blood:	n/a	n/a
39	MAX	chr1:228782406-228784444	HCT-116	colon:	n/a	chr1:228784239-228784249
40	BCL3	chr1:228782408-228783961	A549	lung:	n/a	chr1:228783302-228783315 chr1:228783943-228783956 chr1:228783147-228783156 chr1:228782764-228782773
41	MAX	chr1:228782444-228782789	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr1:228782425-228783175	HCT-116	colon:	n/a	n/a
43	YY1	chr1:228781279-228783085	A549	lung:	n/a	chr1:228781987-228781998 chr1:228781340-228781351 chr1:228782403-228782412 chr1:228781343-228781357 chr1:228781989-228781998 chr1:228781353-228781364 chr1:228781347-228781358
44	POLR2A	chr1:228782353-228785134	MCF10A-Er-Src	breast:	n/a	n/a
45	GTF2F1	chr1:228782495-228784174	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr1:228782288-228782885	SK-N-MC	brain:	n/a	n/a
47	POLR2A	chr1:228782416-228782986	HCT-116	colon:	n/a	n/a
48	ZBTB33	chr1:228782421-228782968	A549	lung:	n/a	n/a
49	FOXA2	chr1:228743895-228782766	A549	lung:	n/a	n/a
50	BACH1	chr1:228782482-228782665	H1-hESC	embryonic stem cell:	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
RNA5S16	TF binding region
DUSP5P1	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	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10753452	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10916338	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12028431	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12035708	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140890	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407568	0.98[ASN][1000 genomes]
rs1925714	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1925717	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1925721	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1925722	0.94[EUR][1000 genomes]
rs2182200	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35598069	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147255	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4147256	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4412590	0.87[EUR][1000 genomes]
rs4653558	0.88[EUR][1000 genomes]
rs4653977	0.86[ASN][1000 genomes]
rs4653979	0.88[ASN][1000 genomes]
rs6426505	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6426507	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670856	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs728964	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415895	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs744668	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7533560	0.90[EUR][1000 genomes];0.84[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228782400-228782600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:228782400-228782600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:228782400-228782600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr1:228782400-228782600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:228782400-228782600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:228782400-228782600	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
7	chr1:228782400-228782600	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr1:228782400-228782600	Active TSS	Primary T cells from cord blood	blood
9	chr1:228782400-228782600	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:228782400-228782600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:228782400-228782600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:228782400-228782600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr1:228782400-228782600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr1:228782400-228782600	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr1:228782400-228782600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:228782400-228782600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:228782400-228782600	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
18	chr1:228782400-228782600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:228782400-228782600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:228782400-228782600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:228782400-228782600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:228782400-228782600	Active TSS	Aorta	Aorta
23	chr1:228782400-228782600	Active TSS	Brain Angular Gyrus	brain
24	chr1:228782400-228782600	Active TSS	Brain Anterior Caudate	brain
25	chr1:228782400-228782600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
26	chr1:228782400-228782600	Active TSS	Brain Hippocampus Middle	brain
27	chr1:228782400-228782600	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr1:228782400-228782600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:228782400-228782600	Active TSS	Brain Substantia Nigra	brain
30	chr1:228782400-228782600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
31	chr1:228782400-228782600	Active TSS	Esophagus	oesophagus
32	chr1:228782400-228782600	Bivalent/Poised TSS	Fetal Brain Female	brain
33	chr1:228782400-228782600	Active TSS	Fetal Heart	heart
34	chr1:228782400-228782600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
35	chr1:228782400-228782600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
36	chr1:228782400-228782600	Active TSS	Fetal Kidney	kidney
37	chr1:228782400-228782600	Bivalent/Poised TSS	Fetal Lung	lung
38	chr1:228782400-228782600	Bivalent/Poised TSS	Fetal Stomach	stomach
39	chr1:228782400-228782600	Enhancers	Gastric	stomach
40	chr1:228782400-228782600	Flanking Active TSS	Left Ventricle	heart
41	chr1:228782400-228782600	Active TSS	Ovary	ovary
42	chr1:228782400-228782600	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:228782400-228782600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
44	chr1:228782400-228782600	Active TSS	Right Atrium	heart
45	chr1:228782400-228782600	Active TSS	Right Ventricle	heart
46	chr1:228782400-228782600	Bivalent/Poised TSS	Stomach Mucosa	stomach
47	chr1:228782400-228782600	Flanking Active TSS	GM12878-XiMat	blood
48	chr1:228782400-228782600	Active TSS	HMEC	breast
49	chr1:228782400-228782600	Active TSS	HSMM	muscle
50	chr1:228782400-228782600	Active TSS	HUVEC	blood vessel

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