Variant report

Variant	rs2072757
Chromosome Location	chr1:169455008-169455009
allele	C/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	ETS1	chr1:169454689-169455506	K562	blood:	n/a	chr1:169455132-169455143
2	PML	chr1:169454817-169455676	MCF-7	breast:	n/a	n/a
3	TFAP2C	chr1:169454455-169455732	Hela-S3	cervix:	n/a	n/a
4	GTF2B	chr1:169454970-169455661	K562	blood:	n/a	n/a
5	TBP	chr1:169454976-169455626	GM12878	blood:	n/a	n/a
6	CCNT2	chr1:169454604-169455681	K562	blood:	n/a	chr1:169455015-169455024
7	MXI1	chr1:169453845-169456810	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr1:169454751-169455777	ProgFib	skin:	n/a	n/a
9	SP1	chr1:169454953-169455615	H1-hESC	embryonic stem cell:	n/a	chr1:169455014-169455026 chr1:169455015-169455024
10	GATA3	chr1:169454978-169455638	T-47D	breast:	n/a	n/a
11	SIN3AK20	chr1:169454997-169455555	HepG2	liver:	n/a	n/a
12	MYC	chr1:169454919-169455545	H1-hESC	embryonic stem cell:	n/a	n/a
13	PBX3	chr1:169454978-169455661	A549	lung:	n/a	n/a
14	CTCF	chr1:169455006-169455637	IMR90	lung:	n/a	n/a
15	CHD1	chr1:169454918-169455619	GM12878	blood:	n/a	chr1:169455009-169455019
16	POLR2A	chr1:169454762-169455717	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr1:169454706-169455491	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:169454742-169455787	SK-N-MC	brain:	n/a	n/a
19	NR3C1	chr1:169454716-169455742	A549	lung:	n/a	chr1:169455115-169455132
20	TAF1	chr1:169454739-169455717	Hela-S3	cervix:	n/a	n/a
21	BRCA1	chr1:169454999-169456158	Hela-S3	cervix:	n/a	n/a
22	TAF1	chr1:169454981-169455651	PFSK-1	brain:	n/a	n/a
23	MAX	chr1:169453879-169456142	Hela-S3	cervix:	n/a	n/a
24	TAF1	chr1:169454493-169455849	ECC-1	luminal epithelium:	n/a	n/a
25	TAF1	chr1:169454974-169455641	Hela-S3	cervix:	n/a	n/a
26	MYC	chr1:169454014-169456207	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr1:169454469-169455761	MCF-7	breast:	n/a	n/a
28	CTCF	chr1:169454963-169455371	K562	blood:	n/a	n/a
29	POLR2A	chr1:169454437-169455995	K562	blood:	n/a	n/a
30	NR3C1	chr1:169454767-169455828	A549	lung:	n/a	chr1:169455115-169455132
31	HEY1	chr1:169454401-169455707	K562	blood:	n/a	chr1:169454753-169454768 chr1:169454781-169454796 chr1:169454742-169454757
32	SP1	chr1:169454968-169455602	GM12878	blood:	n/a	chr1:169455014-169455026 chr1:169455015-169455024
33	E2F6	chr1:169454467-169455717	H1-hESC	embryonic stem cell:	n/a	chr1:169454770-169454782 chr1:169454768-169454783
34	POLR2A	chr1:169454976-169455613	HepG2	liver:	n/a	n/a
35	CREB1	chr1:169454989-169455609	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr1:169454280-169455714	MCF-7	breast:	n/a	n/a
37	ELF1	chr1:169454346-169455616	MCF-7	breast:	n/a	chr1:169455134-169455146 chr1:169455138-169455147 chr1:169455132-169455141
38	MBD4	chr1:169455006-169455718	HepG2	liver:	n/a	n/a
39	MYC	chr1:169454847-169455617	MCF-7	breast:	n/a	n/a
40	MAX	chr1:169454340-169455912	SK-N-SH	brain:	n/a	n/a
41	MAX	chr1:169454274-169455885	A549	lung:	n/a	n/a
42	SRF	chr1:169454752-169455725	MCF-7	breast:	n/a	chr1:169455104-169455118 chr1:169455100-169455118
43	RDBP	chr1:169454757-169455674	K562	blood:	n/a	n/a
44	SP2	chr1:169455000-169455448	K562	blood:	n/a	chr1:169455226-169455241 chr1:169455297-169455307
45	POLR2A	chr1:169454778-169455709	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr1:169452374-169456758	MCF10A-Er-Src	breast:	n/a	n/a
47	NFIC	chr1:169454932-169455820	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr1:169454348-169456091	K562	blood:	n/a	n/a
49	TBP	chr1:169454598-169455891	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr1:169454944-169455731	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169451858..169456935-chr1:169476541..169486862,15	MCF-7	breast:
2	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
3	chr1:169454840..169455424-chr3:156878085..156879028,2	Hela-S3	cervix:
4	chr1:16481268..16482180-chr1:169454924..169455428,2	Hela-S3	cervix:
5	chr1:169454738..169455424-chr1:228783655..228784433,2	Hela-S3	cervix:
6	chr1:169454285..169455235-chr2:20646608..20647266,2	Hela-S3	cervix:
7	chr1:169338121..169342264-chr1:169451874..169455112,4	K562	blood:
8	chr1:169454576..169455277-chr16:2205028..2205838,2	Hela-S3	cervix:
9	chr1:169454417..169455010-chr2:202898201..202898723,2	Hela-S3	cervix:
10	chr1:169454698..169455429-chr15:64752786..64753721,2	Hela-S3	cervix:
11	chr1:16840029..16840801-chr1:169454808..169455627,2	HCT-116	colon:
12	chr1:169454789..169455681-chr12:54385187..54385687,2	Hela-S3	cervix:
13	chr1:169454467..169455010-chr9:132238979..132239886,2	Hela-S3	cervix:
14	chr1:169454326..169457851-chr1:169761976..169765744,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213062	TF binding region
ENSG00000206652	Chromatin interaction
ENSG00000207924	Chromatin interaction
ENSG00000180357	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000198734	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000131653	Chromatin interaction
ENSG00000212237	Chromatin interaction
ENSG00000227959	Chromatin interaction
ENSG00000171806	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000260260	Chromatin interaction
ENSG00000273209	Chromatin interaction
ENSG00000163660	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2038024	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2901092	1.00[CHB][hapmap];0.93[ASN][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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169448000-169457000	Active TSS	Right Ventricle	heart
2	chr1:169450000-169456000	Active TSS	Psoas Muscle	Psoas
3	chr1:169451600-169457000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:169451800-169455400	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr1:169452200-169456200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:169452600-169455600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:169452600-169457000	Active TSS	Left Ventricle	heart
8	chr1:169452800-169455400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:169452800-169455600	Active TSS	HepG2	liver
10	chr1:169452800-169456000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:169452800-169456000	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:169452800-169456200	Active TSS	Ovary	ovary
13	chr1:169453200-169455800	Active TSS	Esophagus	oesophagus
14	chr1:169453200-169456000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:169453200-169456000	Active TSS	Placenta	Placenta
16	chr1:169453200-169456200	Active TSS	Pancreas	Pancrea
17	chr1:169453400-169455800	Active TSS	Fetal Stomach	stomach
18	chr1:169453400-169455800	Active TSS	Lung	lung
19	chr1:169453400-169456000	Active TSS	Colonic Mucosa	Colon
20	chr1:169453400-169456200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:169453400-169456600	Active TSS	Aorta	Aorta
22	chr1:169453600-169455800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:169453600-169456000	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr1:169453600-169456200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:169453600-169457000	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr1:169453600-169457200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:169453800-169455600	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:169453800-169455800	Active TSS	HSMM	muscle
29	chr1:169453800-169456000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr1:169453800-169456200	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:169453800-169456400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr1:169453800-169456400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:169454000-169455600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr1:169454000-169455800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:169454000-169456200	Active TSS	H1 Cell Line	embryonic stem cell
36	chr1:169454000-169456200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:169454000-169456200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr1:169454200-169455600	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr1:169454200-169455600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:169454200-169455600	Active TSS	Muscle Satellite Cultured Cells	--
41	chr1:169454200-169455600	Active TSS	Gastric	stomach
42	chr1:169454200-169455600	Active TSS	Small Intestine	intestine
43	chr1:169454200-169455800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:169454200-169455800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:169454200-169455800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:169454200-169455800	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:169454200-169455800	Active TSS	Brain Germinal Matrix	brain
48	chr1:169454200-169455800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr1:169454200-169455800	Active TSS	Hela-S3	cervix
50	chr1:169454200-169456000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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