Variant report

Variant	rs10035235
Chromosome Location	chr5:40798644-40798645
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	TCF7L2	chr5:40798539-40799053	PANC-1	pancreas:	n/a	n/a
2	ZNF143	chr5:40798055-40799098	Hela-S3	cervix:	n/a	chr5:40798457-40798467 chr5:40798078-40798088 chr5:40798453-40798463 chr5:40798393-40798403
3	MAX	chr5:40797466-40799110	K562	blood:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
4	POLR2A	chr5:40797493-40799044	K562	blood:	n/a	n/a
5	POLR2A	chr5:40798340-40799094	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr5:40797680-40798959	H1-hESC	embryonic stem cell:	n/a	chr5:40798490-40798500 chr5:40798851-40798861
7	POLR2A	chr5:40797547-40799101	K562	blood:	n/a	n/a
8	YY1	chr5:40797590-40798651	K562	blood:	n/a	chr5:40797850-40797864 chr5:40798450-40798464 chr5:40797927-40797936 chr5:40798450-40798461 chr5:40798012-40798023 chr5:40797852-40797861 chr5:40797997-40798008 chr5:40798046-40798057 chr5:40797860-40797871 chr5:40798389-40798403 chr5:40798444-40798458 chr5:40797847-40797861
9	CHD2	chr5:40797532-40799022	K562	blood:	n/a	chr5:40798490-40798500 chr5:40798851-40798861
10	CTCF	chr5:40798095-40799543	K562	blood:	n/a	chr5:40798438-40798451 chr5:40798442-40798451 chr5:40798589-40798598
11	POLR2A	chr5:40797980-40798718	HCT-116	colon:	n/a	n/a
12	POLR2A	chr5:40797957-40798781	PFSK-1	brain:	n/a	n/a
13	MAX	chr5:40797593-40799127	HepG2	liver:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
14	TBL1XR1	chr5:40797271-40799794	K562	blood:	n/a	n/a
15	PML	chr5:40797945-40798713	K562	blood:	n/a	n/a
16	MAZ	chr5:40797297-40799432	IMR90	lung:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
17	MYC	chr5:40797607-40798955	H1-hESC	embryonic stem cell:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
18	ELF1	chr5:40797614-40798928	GM12878	blood:	n/a	chr5:40798106-40798117 chr5:40798106-40798117 chr5:40798107-40798116
19	POLR2A	chr5:40797748-40798707	HepG2	liver:	n/a	n/a
20	RCOR1	chr5:40797576-40800142	K562	blood:	n/a	n/a
21	TAF1	chr5:40797613-40799035	K562	blood:	n/a	n/a
22	RAD21	chr5:40798168-40799131	H1-hESC	embryonic stem cell:	n/a	chr5:40798739-40798749 chr5:40798655-40798665
23	POLR2A	chr5:40798053-40798666	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:40798366-40798924	U87	brain:	n/a	n/a
25	MAZ	chr5:40797598-40798940	GM12878	blood:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
26	CTCF	chr5:40798580-40798730	GM12872	blood:	n/a	chr5:40798589-40798598
27	MXI1	chr5:40797993-40798913	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr5:40797470-40799107	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr5:40798340-40798650	GM12878	blood:	n/a	n/a
30	ZNF384	chr5:40797479-40799069	K562	blood:	n/a	n/a
31	EGR1	chr5:40797994-40798650	H1-hESC	embryonic stem cell:	n/a	chr5:40798300-40798314 chr5:40798452-40798462 chr5:40798330-40798344 chr5:40798519-40798529 chr5:40798079-40798092 chr5:40798485-40798498 chr5:40798454-40798467
32	MAX	chr5:40797585-40799114	MCF-7	breast:	n/a	chr5:40798078-40798088 chr5:40797939-40797948 chr5:40798453-40798463 chr5:40797943-40797952
33	RCOR1	chr5:40798083-40798818	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:40797965-40798733	HUVEC	blood vessel:	n/a	n/a
35	NR2F2	chr5:40797970-40799245	K562	blood:	n/a	n/a
36	POLR2A	chr5:40797598-40798833	Raji	blood:	n/a	n/a
37	POLR2A	chr5:40797950-40798732	HCT-116	colon:	n/a	n/a
38	ELK4	chr5:40798604-40799067	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr5:40798337-40798796	MCF-7	breast:	n/a	chr5:40798438-40798451 chr5:40798442-40798451 chr5:40798589-40798598
40	CTCF	chr5:40798323-40798664	H1-hESC	embryonic stem cell:	n/a	chr5:40798438-40798451 chr5:40798442-40798451 chr5:40798589-40798598
41	SIN3AK20	chr5:40798347-40799111	MCF-7	breast:	n/a	n/a
42	MAX	chr5:40798019-40798818	HepG2	liver:	n/a	chr5:40798078-40798088 chr5:40798453-40798463
43	POLR2A	chr5:40797633-40798707	ProgFib	skin:	n/a	n/a
44	HDAC2	chr5:40797932-40798708	MCF-7	breast:	n/a	n/a
45	ZBTB7A	chr5:40797902-40798822	ECC-1	luminal epithelium:	n/a	n/a
46	E2F4	chr5:40798355-40799397	MCF10A-Er-Src	breast:	n/a	chr5:40798844-40798851 chr5:40798407-40798417 chr5:40798844-40798851 chr5:40798844-40798851 chr5:40798453-40798462 chr5:40798843-40798855 chr5:40798457-40798467 chr5:40798850-40798862 chr5:40798853-40798862
47	MYBL2	chr5:40797969-40798848	HepG2	liver:	n/a	n/a
48	RFX5	chr5:40797380-40799619	Hela-S3	cervix:	n/a	chr5:40797938-40797953 chr5:40797937-40797954 chr5:40798991-40798999 chr5:40797938-40797953 chr5:40797938-40797953
49	BRCA1	chr5:40797611-40799729	Hela-S3	cervix:	n/a	n/a
50	CREB1	chr5:40797960-40799120	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:40755665..40756472-chr5:40798471..40799111,2	K562	blood:
2	chr14:23503156..23503982-chr5:40797904..40798767,2	NB4	blood:
3	chr5:40798207..40798919-chr5:40834882..40835492,2	HCT-116	colon:
4	chr5:40753118..40757884-chr5:40795999..40799979,7	MCF-7	breast:
5	chr11:71823284..71824108-chr5:40797986..40798769,2	Hela-S3	cervix:
6	chr5:40755012..40759487-chr5:40796000..40799940,8	K562	blood:
7	chr5:40796430..40799942-chr5:40831748..40836996,14	MCF-7	breast:
8	chr5:40778589..40781833-chr5:40798494..40800242,3	K562	blood:
9	chr5:40771614..40774420-chr5:40796699..40798889,2	MCF-7	breast:
10	chr5:40752834..40759871-chr5:40793841..40803866,19	K562	blood:
11	chr5:40798384..40799086-chr5:40834783..40835322,2	MCF-7	breast:
12	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:

Variant related genes	Relation type
PRKAA1	TF binding region
ENSG00000212296	Chromatin interaction
ENSG00000100804	Chromatin interaction
ENSG00000113638	Chromatin interaction
ENSG00000110200	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000145592	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10046046	0.86[ASW][hapmap]
rs10053664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10062565	0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs10066459	0.94[JPT][hapmap]
rs10069737	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs1015027	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs10941525	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs11747210	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12514352	0.96[ASN][1000 genomes]
rs12517210	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs12520058	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12523329	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1363847	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs16870407	0.86[ASW][hapmap]
rs16870434	0.86[ASW][hapmap]
rs2270625	0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2291782	0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap]
rs3792824	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792827	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3805489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805492	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805494	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3816959	0.89[JPT][hapmap]
rs4957334	0.94[JPT][hapmap]
rs4957350	0.95[ASN][1000 genomes]
rs62357564	0.96[ASN][1000 genomes]
rs6868112	0.90[JPT][hapmap]
rs72747952	0.81[EUR][1000 genomes]
rs7719692	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7721093	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7725810	0.90[JPT][hapmap]
rs9800106	0.95[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	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
4	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 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	chr5:40795800-40800000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:40796200-40799600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:40796200-40799600	Active TSS	Fetal Intestine Large	intestine
4	chr5:40796400-40799200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr5:40796400-40800000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:40796400-40800000	Active TSS	NHLF	lung
7	chr5:40796600-40798800	Active TSS	Stomach Smooth Muscle	stomach
8	chr5:40796600-40799000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:40796600-40799000	Active TSS	Stomach Mucosa	stomach
10	chr5:40796600-40799000	Active TSS	NH-A	brain
11	chr5:40796600-40799200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:40796600-40799200	Active TSS	Fetal Brain Male	brain
13	chr5:40796600-40799200	Active TSS	Fetal Intestine Small	intestine
14	chr5:40796600-40799200	Active TSS	HSMMtube	muscle
15	chr5:40796600-40799400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:40796600-40799600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:40796600-40799600	Active TSS	Ovary	ovary
18	chr5:40796600-40799800	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr5:40796600-40799800	Active TSS	Fetal Kidney	kidney
20	chr5:40796600-40800000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:40796600-40800400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr5:40796800-40798800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:40796800-40799000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:40796800-40799000	Active TSS	Rectal Smooth Muscle	rectum
25	chr5:40796800-40799200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:40796800-40799200	Active TSS	Aorta	Aorta
27	chr5:40796800-40799200	Active TSS	Fetal Muscle Leg	muscle
28	chr5:40796800-40799200	Active TSS	Psoas Muscle	Psoas
29	chr5:40796800-40799200	Active TSS	Right Ventricle	heart
30	chr5:40796800-40799400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:40796800-40799400	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr5:40796800-40799400	Active TSS	Fetal Stomach	stomach
33	chr5:40796800-40799600	Active TSS	NHDF-Ad	bronchial
34	chr5:40797000-40798800	Active TSS	Placenta	Placenta
35	chr5:40797000-40799000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:40797000-40799000	Active TSS	Fetal Brain Female	brain
37	chr5:40797000-40799000	Active TSS	HSMM	muscle
38	chr5:40797000-40799200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:40797000-40799200	Active TSS	Colonic Mucosa	Colon
40	chr5:40797000-40799200	Active TSS	Fetal Muscle Trunk	muscle
41	chr5:40797000-40799200	Active TSS	Thymus	Thymus
42	chr5:40797000-40799400	Active TSS	K562	blood
43	chr5:40797000-40799800	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr5:40797000-40800000	Active TSS	H1 Cell Line	embryonic stem cell
45	chr5:40797200-40798800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:40797200-40798800	Active TSS	Small Intestine	intestine
47	chr5:40797200-40799000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr5:40797200-40799000	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr5:40797200-40799000	Active TSS	Brain Germinal Matrix	brain
50	chr5:40797200-40799000	Active TSS	Brain Substantia Nigra	brain

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