Variant report

Variant	rs4653641
Chromosome Location	chr1:225653090-225653091
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	POLR2A	chr1:225652612-225653522	Hela-S3	cervix:	n/a	n/a
2	USF2	chr1:225653044-225653459	Hela-S3	cervix:	n/a	n/a
3	CHD2	chr1:225652644-225653524	Hela-S3	cervix:	n/a	n/a
4	RFX5	chr1:225652584-225653530	Hela-S3	cervix:	n/a	n/a
5	ZKSCAN1	chr1:225652843-225653418	Hela-S3	cervix:	n/a	n/a
6	MAFK	chr1:225652660-225653474	Hela-S3	cervix:	n/a	n/a
7	ZNF143	chr1:225652588-225653509	Hela-S3	cervix:	n/a	chr1:225653269-225653288
8	TFAP2A	chr1:225652680-225653795	Hela-S3	cervix:	n/a	chr1:225653222-225653232 chr1:225653222-225653232 chr1:225653220-225653234 chr1:225653222-225653232 chr1:225653220-225653235
9	SMARCC1	chr1:225652648-225653667	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:225652654-225653483	Hela-S3	cervix:	n/a	n/a
11	TBP	chr1:225652832-225653443	Hela-S3	cervix:	n/a	n/a
12	CREB1	chr1:225652418-225653262	H1-hESC	embryonic stem cell:	n/a	n/a
13	MYC	chr1:225652605-225653483	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:225652751-225653453	Hela-S3	cervix:	n/a	n/a
15	FOS	chr1:225653071-225653377	MCF10A-Er-Src	breast:	n/a	n/a
16	MXI1	chr1:225652646-225653513	Hela-S3	cervix:	n/a	n/a
17	EP300	chr1:225653000-225653433	Hela-S3	cervix:	n/a	n/a
18	TFAP2C	chr1:225652593-225653834	Hela-S3	cervix:	n/a	chr1:225653220-225653235 chr1:225653054-225653063
19	MAX	chr1:225652675-225653525	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr1:225652781-225653495	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr1:225652314-225653840	Hela-S3	cervix:	n/a	n/a
22	MYC	chr1:225653088-225653467	MCF10A-Er-Src	breast:	n/a	n/a
23	BRCA1	chr1:225653015-225653483	Hela-S3	cervix:	n/a	n/a
24	ZNF263	chr1:225652611-225653640	HEK293-T-REx	kidney:	n/a	n/a
25	TCF12	chr1:225652870-225653522	ECC-1	luminal epithelium:	n/a	n/a
26	MAZ	chr1:225652763-225653537	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:225652725-225653556	Hela-S3	cervix:	n/a	n/a
28	SMC3	chr1:225652648-225653576	Hela-S3	cervix:	n/a	n/a
29	MAX	chr1:225652751-225653478	Hela-S3	cervix:	n/a	n/a
30	RAD21	chr1:225653033-225653474	Hela-S3	cervix:	n/a	n/a
31	NFYA	chr1:225652999-225653339	Hela-S3	cervix:	n/a	n/a
32	RCOR1	chr1:225652743-225653575	Hela-S3	cervix:	n/a	n/a
33	TCF7L2	chr1:225652689-225653562	Hela-S3	cervix:	n/a	n/a
34	GTF2F1	chr1:225652780-225653461	Hela-S3	cervix:	n/a	n/a
35	ELK1	chr1:225652562-225653424	Hela-S3	cervix:	n/a	n/a
36	KAP1	chr1:225652624-225653218	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:225652849..225654996-chr1:225964946..225967311,2	MCF-7	breast:
2	chr1:225652711..225653212-chr6:26216728..26217456,2	Hela-S3	cervix:
3	chr1:225652465..225653214-chr21:44312715..44313565,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000234476	TF binding region
ENSG00000168274	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000160194	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1764344	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1771315	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131411	1.00[AMR][1000 genomes]
rs2615065	1.00[AMR][1000 genomes]
rs2615072	1.00[AMR][1000 genomes]
rs2639717	1.00[AMR][1000 genomes]
rs2657565	1.00[AMR][1000 genomes]
rs2840947	1.00[AMR][1000 genomes]
rs2840951	1.00[AMR][1000 genomes]
rs2840961	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6703803	1.00[EUR][1000 genomes]
rs73138909	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225642400-225655200	Weak transcription	Small Intestine	intestine
2	chr1:225642600-225655000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:225646400-225653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225647000-225653600	Enhancers	Esophagus	oesophagus
5	chr1:225647000-225654600	Enhancers	Fetal Thymus	thymus
6	chr1:225647000-225654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:225647400-225654800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:225647600-225653800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:225647800-225653400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:225648400-225653400	Weak transcription	Fetal Intestine Large	intestine
11	chr1:225648800-225654600	Weak transcription	HUVEC	blood vessel
12	chr1:225649000-225653200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:225649000-225654600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:225649200-225654400	Weak transcription	Primary T cells from cord blood	blood
15	chr1:225649400-225653400	Weak transcription	Dnd41	blood
16	chr1:225649800-225654800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:225649800-225662600	Weak transcription	Pancreas	Pancrea
18	chr1:225650000-225653200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:225650000-225653600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:225650200-225653200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:225650200-225653200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:225650200-225653800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:225650200-225654600	Weak transcription	Spleen	Spleen
24	chr1:225650600-225653600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr1:225650800-225653600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr1:225650800-225653600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:225650800-225653800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:225651000-225653200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr1:225651000-225653600	Enhancers	HMEC	breast
30	chr1:225651200-225653200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:225651200-225653400	Weak transcription	Right Atrium	heart
32	chr1:225651200-225655200	Weak transcription	Right Ventricle	heart
33	chr1:225651400-225653600	Weak transcription	Thymus	Thymus
34	chr1:225651400-225654600	Weak transcription	Lung	lung
35	chr1:225651400-225662400	Weak transcription	Fetal Brain Male	brain
36	chr1:225651600-225653200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:225651600-225654400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:225651600-225655000	Weak transcription	Stomach Mucosa	stomach
39	chr1:225651600-225655200	Weak transcription	Fetal Intestine Small	intestine
40	chr1:225651800-225653200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:225651800-225653800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:225651800-225654800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:225652000-225653200	Weak transcription	Brain Germinal Matrix	brain
44	chr1:225652000-225653600	Enhancers	Fetal Muscle Leg	muscle
45	chr1:225652000-225653600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:225652000-225653800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:225652000-225654400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:225652000-225655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:225652200-225653400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:225652200-225653800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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