Variant report

Variant	rs4149855
Chromosome Location	chr1:242012606-242012607
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	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	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
5	UBTF	chr1:242010695-242012711	K562	blood:	n/a	n/a
6	MXI1	chr1:242010563-242013411	SK-N-SH	brain:	n/a	n/a
7	CUX1	chr1:242009983-242013139	K562	blood:	n/a	n/a
8	KAP1	chr1:242010758-242012816	HEK293	kidney:	n/a	n/a
9	TBL1XR1	chr1:242010817-242012680	K562	blood:	n/a	n/a
10	JUND	chr1:242009855-242012643	K562	blood:	n/a	chr1:242010675-242010684
11	POLR2A	chr1:242010335-242013165	GM12891	blood:	n/a	n/a
12	SMC3	chr1:242010850-242012872	Hela-S3	cervix:	n/a	chr1:242011419-242011429
13	POLR2A	chr1:242010107-242012967	PBDE	blood:	n/a	n/a
14	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
15	POLR2A	chr1:242010531-242012942	Hela-S3	cervix:	n/a	n/a
16	MAX	chr1:242011009-242013216	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:242010979-242013124	Hela-S3	cervix:	n/a	n/a
18	MAX	chr1:242010672-242012608	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr1:242010843-242012887	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr1:242012438-242012806	Hela-S3	cervix:	n/a	chr1:242012592-242012605
21	TBP	chr1:242010254-242012925	K562	blood:	n/a	n/a
22	ZNF263	chr1:242010966-242013144	HEK293-T-REx	kidney:	n/a	chr1:242011628-242011637
23	EP300	chr1:242010412-242012800	K562	blood:	n/a	chr1:242012590-242012604 chr1:242010605-242010619
24	POLR2A	chr1:242010299-242013215	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	chr1:242012601..242013405-chr1:242037363..242038255,2	MCF-7	breast:
4	chr1:242010666..242013007-chr1:242013453..242016461,3	MCF-7	breast:
5	chr1:241799658..241805161-chr1:242010004..242013743,14	K562	blood:
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
ENSG00000162843	Chromatin interaction
ENSG00000117009	Chromatin interaction
ENSG00000174371	Chromatin interaction
ENSG00000054277	Chromatin interaction
ENSG00000091483	Chromatin interaction
ENSG00000203668	Chromatin interaction
ENSG00000153187	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12138714	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12562788	0.96[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];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298932	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298933	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298935	0.96[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35245437	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3819355	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[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];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819359	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3819360	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4149852	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]
rs4149853	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4149863	0.94[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4149869	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149871	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149872	0.83[AFR][1000 genomes]
rs4149876	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149878	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149885	0.83[AFR][1000 genomes]
rs4149889	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149890	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149891	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149896	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149900	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149919	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149921	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149927	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4149934	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4149938	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4149948	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4149963	0.83[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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242010600-242012800	Active TSS	HSMM	muscle
2	chr1:242010600-242013200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:242010800-242012800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:242010800-242012800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:242010800-242013000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:242010800-242013000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:242010800-242013000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:242011000-242013000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:242011200-242012800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:242011600-242012800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr1:242011600-242012800	Flanking Active TSS	Osteobl	bone
12	chr1:242011800-242012800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr1:242011800-242012800	Flanking Active TSS	Fetal Stomach	stomach
14	chr1:242011800-242012800	Enhancers	Small Intestine	intestine
15	chr1:242011800-242012800	Flanking Active TSS	NHEK	skin
16	chr1:242011800-242013000	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr1:242011800-242013200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:242011800-242013200	Flanking Active TSS	HUVEC	blood vessel
19	chr1:242012000-242012800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:242012000-242012800	Flanking Active TSS	HepG2	liver
21	chr1:242012000-242012800	Flanking Active TSS	NHLF	lung
22	chr1:242012000-242013000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr1:242012000-242013000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:242012000-242013000	Enhancers	Placenta	Placenta
25	chr1:242012000-242013200	Transcr. at gene 5' and 3'	K562	blood
26	chr1:242012000-242014000	Transcr. at gene 5' and 3'	Dnd41	blood
27	chr1:242012000-242021400	Weak transcription	Right Atrium	heart
28	chr1:242012000-242023800	Weak transcription	Stomach Mucosa	stomach
29	chr1:242012000-242032600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:242012200-242012800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:242012200-242012800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:242012200-242012800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:242012200-242012800	Active TSS	Fetal Intestine Small	intestine
34	chr1:242012200-242012800	Active TSS	Fetal Kidney	kidney
35	chr1:242012200-242013000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:242012200-242013000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:242012200-242013000	Weak transcription	Esophagus	oesophagus
38	chr1:242012200-242013000	Enhancers	Placenta Amnion	Placenta Amnion
39	chr1:242012200-242013000	Flanking Active TSS	Hela-S3	cervix
40	chr1:242012200-242013200	Transcr. at gene 5' and 3'	A549	lung
41	chr1:242012200-242013200	Active TSS	NH-A	brain
42	chr1:242012200-242016800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:242012200-242025600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:242012200-242027800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:242012200-242028600	Weak transcription	Gastric	stomach
46	chr1:242012200-242044000	Weak transcription	Primary B cells from cord blood	blood
47	chr1:242012400-242012800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr1:242012400-242012800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:242012400-242012800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:242012400-242012800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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