Variant report

Variant	rs1635517
Chromosome Location	chr1:242012033-242012034
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	E2F4	chr1:242010948-242012174	Hela-S3	cervix:	n/a	chr1:242011510-242011517 chr1:242011508-242011519 chr1:242011510-242011517 chr1:242011510-242011518 chr1:242011509-242011519 chr1:242011510-242011517 chr1:242011484-242011498 chr1:242011450-242011459 chr1:242011452-242011461 chr1:242011509-242011520 chr1:242011510-242011521 chr1:242011510-242011518
2	ZMIZ1	chr1:242010273-242012107	K562	blood:	n/a	n/a
3	HMGN3	chr1:242011078-242012050	K562	blood:	n/a	n/a
4	RCOR1	chr1:242010776-242012810	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chr1:242010075-242012914	K562	blood:	n/a	n/a
6	SIN3AK20	chr1:242010868-242012157	HCT-116	colon:	n/a	n/a
7	HCFC1	chr1:242010611-242012901	Hela-S3	cervix:	n/a	n/a
8	IRF1	chr1:242009937-242012536	K562	blood:	n/a	chr1:242011465-242011479 chr1:242011421-242011435
9	GATA2	chr1:242010654-242012633	SH-SY5Y	brain:	n/a	chr1:242011881-242011891 chr1:242011883-242011890 chr1:242012553-242012563 chr1:242011883-242011890 chr1:242011881-242011890 chr1:242012490-242012507 chr1:242011883-242011890
10	POLR2A	chr1:242010099-242012264	K562	blood:	n/a	n/a
11	E2F6	chr1:242009991-242012325	K562	blood:	n/a	chr1:242011510-242011517 chr1:242011510-242011517 chr1:242011510-242011518 chr1:242011509-242011519 chr1:242011510-242011517 chr1:242011484-242011498 chr1:242011450-242011459 chr1:242011452-242011461 chr1:242011509-242011520 chr1:242011510-242011521 chr1:242011510-242011518
12	UBTF	chr1:242010695-242012711	K562	blood:	n/a	n/a
13	STAT5A	chr1:242010513-242012131	K562	blood:	n/a	chr1:242011749-242011758 chr1:242011748-242011757
14	MYC	chr1:242011995-242012407	MCF10A-Er-Src	breast:	n/a	n/a
15	MXI1	chr1:242010563-242013411	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr1:242010871-242012142	HL-60	blood:	n/a	n/a
17	POLR2A	chr1:242010965-242012319	HEK293	kidney:	n/a	n/a
18	ELF1	chr1:242010943-242012060	K562	blood:	n/a	n/a
19	CUX1	chr1:242009983-242013139	K562	blood:	n/a	n/a
20	POLR2A	chr1:242010407-242012518	K562	blood:	n/a	n/a
21	POLR2A	chr1:242010551-242012103	K562	blood:	n/a	n/a
22	YY1	chr1:242012004-242012208	K562	blood:	n/a	n/a
23	NR2F2	chr1:242010214-242012402	K562	blood:	n/a	n/a
24	MAX	chr1:242010869-242012435	A549	lung:	n/a	n/a
25	KAP1	chr1:242010758-242012816	HEK293	kidney:	n/a	n/a
26	HEY1	chr1:242010566-242012257	K562	blood:	n/a	chr1:242011452-242011461
27	POLR2A	chr1:242011120-242012042	HepG2	liver:	n/a	n/a
28	MYC	chr1:242010906-242012321	NB4	blood:	n/a	n/a
29	POLR2A	chr1:242010728-242012231	K562	blood:	n/a	n/a
30	POLR2A	chr1:242010881-242012231	GM12878	blood:	n/a	n/a
31	MAZ	chr1:242010035-242012545	K562	blood:	n/a	n/a
32	POLR2A	chr1:242010545-242012198	K562	blood:	n/a	n/a
33	MAX	chr1:242010175-242012311	K562	blood:	n/a	n/a
34	POLR2A	chr1:242010903-242012126	GM18951	blood:	n/a	n/a
35	POLR2A	chr1:242010536-242012377	H1-hESC	embryonic stem cell:	n/a	n/a
36	SIN3AK20	chr1:242010803-242012055	MCF-7	breast:	n/a	n/a
37	SIN3A	chr1:242011010-242012245	GM12878	blood:	n/a	n/a
38	TCF7L2	chr1:242010973-242012141	Hela-S3	cervix:	n/a	n/a
39	MAZ	chr1:242010577-242012274	IMR90	lung:	n/a	n/a
40	CEBPB	chr1:242010917-242012153	Hela-S3	cervix:	n/a	n/a
41	SMARCB1	chr1:242010831-242012182	Hela-S3	cervix:	n/a	n/a
42	MXI1	chr1:242010858-242012542	Hela-S3	cervix:	n/a	n/a
43	IRF1	chr1:242010158-242012313	K562	blood:	n/a	chr1:242011465-242011479 chr1:242011421-242011435
44	PML	chr1:242010674-242012229	K562	blood:	n/a	n/a
45	MXI1	chr1:242010493-242012416	IMR90	lung:	n/a	n/a
46	NR2F2	chr1:242010980-242012173	K562	blood:	n/a	n/a
47	TBL1XR1	chr1:242010817-242012680	K562	blood:	n/a	n/a
48	JUND	chr1:242009855-242012643	K562	blood:	n/a	chr1:242010675-242010684
49	MXI1	chr1:242010998-242012111	HepG2	liver:	n/a	n/a
50	POLR2A	chr1:242010924-242012104	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:241680902..241684541-chr1:242009942..242012706,4	K562	blood:
2	chr1:241681898..241684060-chr1:242010602..242013002,4	K562	blood:
3	chr1:242010666..242013007-chr1:242013453..242016461,3	MCF-7	breast:
4	chr1:241799658..241805161-chr1:242010004..242013743,14	K562	blood:
5	chr1:241798094..241801033-chr1:242010173..242012572,2	MCF-7	breast:
6	chr1:241814475..241817056-chr1:242011284..242012979,2	K562	blood:
7	chr1:242011304..242012261-chr22:45559835..45560477,2	Hela-S3	cervix:
8	chr1:241814475..241817056-chr1:242011284..242013767,3	K562	blood:
9	chr1:241692902..241697485-chr1:242010276..242014432,6	K562	blood:
10	chr1:241693547..241697485-chr1:242010276..242012986,4	K562	blood:
11	chr1:242011682..242012300-chr13:107220012..107220532,2	Hela-S3	cervix:
12	chr1:242009986..242012755-chr1:245025033..245026742,2	K562	blood:
13	chr1:241796724..241805103-chr1:242008052..242013159,15	K562	blood:

Variant related genes	Relation type
EXO1	TF binding region
ENSG00000117009	Chromatin interaction
ENSG00000174371	Chromatin interaction
ENSG00000162843	Chromatin interaction
ENSG00000054277	Chromatin interaction
ENSG00000153187	Chromatin interaction
ENSG00000093000	Chromatin interaction
ENSG00000203668	Chromatin interaction
ENSG00000091483	Chromatin interaction
ENSG00000134884	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1627006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1629051	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1635501	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1635502	0.90[CEU][hapmap];0.93[CHB][hapmap];0.85[EUR][1000 genomes]
rs1635507	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1635509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1635511	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1635512	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1635515	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1776131	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1776132	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1776133	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1776134	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1776135	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1776137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1776178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1776180	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1776181	0.83[MKK][hapmap]
rs2236918	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236919	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2488471	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2488472	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2526697	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs2526699	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526701	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526704	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2995544	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs735943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs851780	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs851782	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv528015	chr1:241865219-242070731	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv2762521	chr1:241891040-242074222	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv873373	chr1:241939069-242027500	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv873374	chr1:241975147-242097624	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242010600-242012200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:242010600-242012200	Active TSS	Rectal Smooth Muscle	rectum
3	chr1:242010600-242012400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:242010600-242012400	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:242010600-242012400	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:242010600-242012400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:242010600-242012600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:242010600-242012800	Active TSS	HSMM	muscle
9	chr1:242010600-242013200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:242010800-242012200	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr1:242010800-242012200	Active TSS	A549	lung
12	chr1:242010800-242012400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr1:242010800-242012600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:242010800-242012600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:242010800-242012600	Active TSS	NHDF-Ad	bronchial
16	chr1:242010800-242012800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:242010800-242012800	Active TSS	H9 Cell Line	embryonic stem cell
18	chr1:242010800-242013000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:242010800-242013000	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:242010800-242013000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:242011000-242012200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:242011000-242012200	Active TSS	Hela-S3	cervix
23	chr1:242011000-242012200	Active TSS	HSMMtube	muscle
24	chr1:242011000-242012400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr1:242011000-242012400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr1:242011000-242012400	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr1:242011000-242012400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:242011000-242012400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:242011000-242012400	Active TSS	GM12878-XiMat	blood
30	chr1:242011000-242012600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:242011000-242013000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:242011200-242012800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:242011600-242012200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:242011600-242012200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:242011600-242012200	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr1:242011600-242012200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:242011600-242012200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr1:242011600-242012200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr1:242011600-242012200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:242011600-242012200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:242011600-242012200	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr1:242011600-242012200	Flanking Active TSS	Fetal Brain Female	brain
43	chr1:242011600-242012200	Flanking Active TSS	Fetal Intestine Small	intestine
44	chr1:242011600-242012200	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr1:242011600-242012200	Flanking Active TSS	Fetal Thymus	thymus
46	chr1:242011600-242012200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:242011600-242012200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr1:242011600-242012400	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr1:242011600-242012400	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr1:242011600-242012600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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