Variant report

Variant	rs4149852
Chromosome Location	chr1:242012385-242012386
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	RCOR1	chr1:242010776-242012810	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr1:242010075-242012914	K562	blood:	n/a	n/a
3	HCFC1	chr1:242010611-242012901	Hela-S3	cervix:	n/a	n/a
4	IRF1	chr1:242009937-242012536	K562	blood:	n/a	chr1:242011465-242011479 chr1:242011421-242011435
5	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
6	UBTF	chr1:242010695-242012711	K562	blood:	n/a	n/a
7	MYC	chr1:242011995-242012407	MCF10A-Er-Src	breast:	n/a	n/a
8	MXI1	chr1:242010563-242013411	SK-N-SH	brain:	n/a	n/a
9	CUX1	chr1:242009983-242013139	K562	blood:	n/a	n/a
10	POLR2A	chr1:242010407-242012518	K562	blood:	n/a	n/a
11	NR2F2	chr1:242010214-242012402	K562	blood:	n/a	n/a
12	MAX	chr1:242010869-242012435	A549	lung:	n/a	n/a
13	KAP1	chr1:242010758-242012816	HEK293	kidney:	n/a	n/a
14	MAZ	chr1:242010035-242012545	K562	blood:	n/a	n/a
15	MXI1	chr1:242010858-242012542	Hela-S3	cervix:	n/a	n/a
16	MAZ	chr1:242012076-242012505	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr1:242010493-242012416	IMR90	lung:	n/a	n/a
18	TBL1XR1	chr1:242010817-242012680	K562	blood:	n/a	n/a
19	JUND	chr1:242009855-242012643	K562	blood:	n/a	chr1:242010675-242010684
20	POLR2A	chr1:242010335-242013165	GM12891	blood:	n/a	n/a
21	SMC3	chr1:242010850-242012872	Hela-S3	cervix:	n/a	chr1:242011419-242011429
22	POLR2A	chr1:242010107-242012967	PBDE	blood:	n/a	n/a
23	CREB1	chr1:242010409-242012447	K562	blood:	n/a	chr1:242011449-242011462
24	E2F4	chr1:242010567-242013180	MCF10A-Er-Src	breast:	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
25	GATA3	chr1:242012138-242012508	SH-SY5Y	brain:	n/a	chr1:242012490-242012507
26	CBX3	chr1:242009636-242012532	K562	blood:	n/a	n/a
27	POLR2A	chr1:242010531-242012942	Hela-S3	cervix:	n/a	n/a
28	MAX	chr1:242011009-242013216	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr1:242010979-242013124	Hela-S3	cervix:	n/a	n/a
30	MAX	chr1:242010672-242012608	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr1:242010063-242012428	K562	blood:	n/a	n/a
32	MAFK	chr1:242010775-242012421	Hela-S3	cervix:	n/a	n/a
33	GTF2F1	chr1:242010843-242012887	Hela-S3	cervix:	n/a	n/a
34	TBP	chr1:242010254-242012925	K562	blood:	n/a	n/a
35	ZNF263	chr1:242010966-242013144	HEK293-T-REx	kidney:	n/a	chr1:242011628-242011637
36	EP300	chr1:242010412-242012800	K562	blood:	n/a	chr1:242012590-242012604 chr1:242010605-242010619
37	POLR2A	chr1:242010299-242013215	K562	blood:	n/a	n/a
38	BHLHE40	chr1:242010326-242012591	K562	blood:	n/a	chr1:242011324-242011340
39	SIN3A	chr1:242010989-242012497	H1-hESC	embryonic stem cell:	n/a	n/a
40	GATA1	chr1:242009980-242012564	PBDE	blood:	n/a	chr1:242011881-242011891 chr1:242011883-242011890 chr1:242012553-242012563 chr1:242010607-242010617 chr1:242011883-242011890 chr1:242011881-242011890 chr1:242012490-242012507 chr1:242011883-242011890
41	MYC	chr1:242010091-242012388	K562	blood:	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	chr1:241814475..241817056-chr1:242011284..242013767,3	K562	blood:
8	chr1:241692902..241697485-chr1:242010276..242014432,6	K562	blood:
9	chr1:241693547..241697485-chr1:242010276..242012986,4	K562	blood:
10	chr1:242009986..242012755-chr1:245025033..245026742,2	K562	blood:
11	chr1:241796724..241805103-chr1:242008052..242013159,15	K562	blood:

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

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

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

rs_ID	r²[population]
rs12138714	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12562788	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298932	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298933	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298935	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35245437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3819355	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819357	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819359	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819360	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4149855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149869	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149871	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149876	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149878	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149889	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149890	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149891	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149896	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149900	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149919	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149921	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149927	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4149934	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149938	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4149948	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4149963	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242010600-242012400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:242010600-242012400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:242010600-242012400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr1:242010600-242012400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:242010600-242012600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:242010600-242012800	Active TSS	HSMM	muscle
7	chr1:242010600-242013200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:242010800-242012400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr1:242010800-242012600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:242010800-242012600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:242010800-242012600	Active TSS	NHDF-Ad	bronchial
12	chr1:242010800-242012800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:242010800-242012800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr1:242010800-242013000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:242010800-242013000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:242010800-242013000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:242011000-242012400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr1:242011000-242012400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:242011000-242012400	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:242011000-242012400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:242011000-242012400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:242011000-242012400	Active TSS	GM12878-XiMat	blood
23	chr1:242011000-242012600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:242011000-242013000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:242011200-242012800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:242011600-242012400	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:242011600-242012400	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr1:242011600-242012600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:242011600-242012600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:242011600-242012600	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr1:242011600-242012800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr1:242011600-242012800	Flanking Active TSS	Osteobl	bone
33	chr1:242011800-242012400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:242011800-242012400	Flanking Active TSS	Fetal Heart	heart
35	chr1:242011800-242012600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:242011800-242012600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr1:242011800-242012800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr1:242011800-242012800	Flanking Active TSS	Fetal Stomach	stomach
39	chr1:242011800-242012800	Enhancers	Small Intestine	intestine
40	chr1:242011800-242012800	Flanking Active TSS	NHEK	skin
41	chr1:242011800-242013000	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr1:242011800-242013200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:242011800-242013200	Flanking Active TSS	HUVEC	blood vessel
44	chr1:242012000-242012600	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr1:242012000-242012800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:242012000-242012800	Flanking Active TSS	HepG2	liver
47	chr1:242012000-242012800	Flanking Active TSS	NHLF	lung
48	chr1:242012000-242013000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr1:242012000-242013000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:242012000-242013000	Enhancers	Placenta	Placenta

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