Variant report

Variant	rs7435941
Chromosome Location	chr4:57300930-57300931
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	MXI1	chr4:57300894-57303518	HepG2	liver:	n/a	n/a
2	MXI1	chr4:57300786-57304245	IMR90	lung:	n/a	n/a
3	POLR2A	chr4:57300776-57302830	PBDE	blood:	n/a	n/a
4	SIN3AK20	chr4:57300888-57302916	K562	blood:	n/a	n/a
5	RCOR1	chr4:57300494-57302764	K562	blood:	n/a	n/a
6	PML	chr4:57300757-57303712	GM12878	blood:	n/a	n/a
7	TBP	chr4:57300179-57301315	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr4:57300894-57303737	IMR90	lung:	n/a	n/a
9	RFX5	chr4:57300370-57301162	Hela-S3	cervix:	n/a	chr4:57300987-57301004
10	MXI1	chr4:57300482-57302815	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr4:57300909-57302793	Hela-S3	cervix:	n/a	n/a
12	UBTF	chr4:57299970-57302790	K562	blood:	n/a	n/a
13	MAX	chr4:57300846-57302968	ECC-1	luminal epithelium:	n/a	chr4:57302554-57302564 chr4:57301487-57301497 chr4:57302555-57302564 chr4:57301655-57301666 chr4:57301657-57301664 chr4:57302623-57302632 chr4:57302554-57302565 chr4:57301656-57301665 chr4:57301655-57301665 chr4:57302555-57302564 chr4:57302556-57302563 chr4:57301957-57301964
14	TBP	chr4:57300868-57302689	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr4:57300765-57302972	HepG2	liver:	n/a	chr4:57302554-57302564 chr4:57301487-57301497 chr4:57302555-57302564 chr4:57301655-57301666 chr4:57301657-57301664 chr4:57302623-57302632 chr4:57302554-57302565 chr4:57301656-57301665 chr4:57301655-57301665 chr4:57302555-57302564 chr4:57302556-57302563 chr4:57301957-57301964
16	MAX	chr4:57300863-57302952	HepG2	liver:	n/a	chr4:57302554-57302564 chr4:57301487-57301497 chr4:57302555-57302564 chr4:57301655-57301666 chr4:57301657-57301664 chr4:57302623-57302632 chr4:57302554-57302565 chr4:57301656-57301665 chr4:57301655-57301665 chr4:57302555-57302564 chr4:57302556-57302563 chr4:57301957-57301964
17	CUX1	chr4:57300347-57301148	K562	blood:	n/a	n/a
18	TBP	chr4:57300836-57302868	K562	blood:	n/a	n/a
19	NFYB	chr4:57300868-57301329	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr4:57300889-57302944	Hela-S3	cervix:	n/a	n/a
21	HCFC1	chr4:57300928-57302797	K562	blood:	n/a	n/a
22	MTA3	chr4:57300867-57302949	GM12878	blood:	n/a	n/a
23	POLR2A	chr4:57300923-57303500	Raji	blood:	n/a	n/a
24	POLR2A	chr4:57300879-57302844	K562	blood:	n/a	n/a
25	MAX	chr4:57300848-57302931	ECC-1	luminal epithelium:	n/a	chr4:57302554-57302564 chr4:57301487-57301497 chr4:57302555-57302564 chr4:57301655-57301666 chr4:57301657-57301664 chr4:57302623-57302632 chr4:57302554-57302565 chr4:57301656-57301665 chr4:57301655-57301665 chr4:57302555-57302564 chr4:57302556-57302563 chr4:57301957-57301964
26	JUND	chr4:57300219-57302743	K562	blood:	n/a	chr4:57301262-57301271 chr4:57302581-57302590
27	POLR2A	chr4:57300845-57304323	GM12892	blood:	n/a	n/a
28	TBP	chr4:57300877-57302891	HepG2	liver:	n/a	n/a
29	POLR2A	chr4:57300848-57304432	SK-N-MC	brain:	n/a	n/a
30	SIN3A	chr4:57300907-57302843	GM12878	blood:	n/a	chr4:57301877-57301888
31	MYC	chr4:57300927-57302845	K562	blood:	n/a	chr4:57302554-57302564 chr4:57301487-57301497 chr4:57302555-57302564 chr4:57301655-57301666 chr4:57301657-57301664 chr4:57302623-57302632 chr4:57302554-57302565 chr4:57301656-57301665 chr4:57301655-57301665 chr4:57302555-57302564 chr4:57302556-57302563 chr4:57301957-57301964
32	MAX	chr4:57300867-57302857	K562	blood:	n/a	chr4:57302554-57302564 chr4:57301487-57301497 chr4:57302555-57302564 chr4:57301655-57301666 chr4:57301657-57301664 chr4:57302623-57302632 chr4:57302554-57302565 chr4:57301656-57301665 chr4:57301655-57301665 chr4:57302555-57302564 chr4:57302556-57302563 chr4:57301957-57301964
33	POLR2A	chr4:57300795-57300936	HepG2	liver:	n/a	n/a
34	RUNX3	chr4:57300835-57302787	GM12878	blood:	n/a	n/a
35	BHLHE40	chr4:57300883-57302862	GM12878	blood:	n/a	n/a
36	POLR2A	chr4:57300813-57303564	HepG2	liver:	n/a	n/a
37	SP1	chr4:57300930-57302767	A549	lung:	n/a	chr4:57301883-57301895 chr4:57301264-57301273 chr4:57301884-57301894 chr4:57301262-57301274 chr4:57302579-57302593 chr4:57301264-57301273 chr4:57301884-57301893 chr4:57301883-57301895 chr4:57301885-57301894 chr4:57302163-57302172 chr4:57301885-57301894 chr4:57302161-57302173 chr4:57301262-57301274 chr4:57302161-57302173 chr4:57301263-57301272 chr4:57301880-57301894 chr4:57301827-57301841
38	CHD1	chr4:57300919-57303706	H1-hESC	embryonic stem cell:	n/a	chr4:57301264-57301274
39	POLR2A	chr4:57300728-57303893	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr4:57300918-57302943	K562	blood:	n/a	n/a
41	POLR2A	chr4:57300758-57302852	HUVEC	blood vessel:	n/a	n/a
42	UBTF	chr4:57300590-57302764	K562	blood:	n/a	n/a
43	HEY1	chr4:57300864-57302892	HepG2	liver:	n/a	chr4:57301852-57301867
44	MAX	chr4:57300911-57302958	MCF-7	breast:	n/a	chr4:57302554-57302564 chr4:57301487-57301497 chr4:57302555-57302564 chr4:57301655-57301666 chr4:57301657-57301664 chr4:57302623-57302632 chr4:57302554-57302565 chr4:57301656-57301665 chr4:57301655-57301665 chr4:57302555-57302564 chr4:57302556-57302563 chr4:57301957-57301964
45	POLR2A	chr4:57300852-57302795	H1-neurons	neurons:	n/a	n/a
46	TAF1	chr4:57300851-57303034	ECC-1	luminal epithelium:	n/a	n/a
47	HEY1	chr4:57300783-57302945	K562	blood:	n/a	chr4:57301852-57301867
48	POLR2A	chr4:57300296-57303752	H1-hESC	embryonic stem cell:	n/a	n/a
49	E2F6	chr4:57300903-57302828	H1-hESC	embryonic stem cell:	n/a	chr4:57302566-57302575 chr4:57301077-57301084 chr4:57301075-57301085 chr4:57301076-57301084 chr4:57301784-57301793 chr4:57301076-57301085 chr4:57301073-57301084 chr4:57301076-57301084 chr4:57301077-57301084 chr4:57301263-57301272 chr4:57301074-57301085 chr4:57301077-57301084 chr4:57301263-57301275
50	POLR2A	chr4:57300870-57302870	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57252573..57255971-chr4:57298663..57303783,6	MCF-7	breast:
2	chr4:56411581..56413941-chr4:57300856..57302618,2	K562	blood:
3	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
4	chr4:57298757..57303397-chr4:57395270..57398462,7	K562	blood:
5	chr4:57275711..57277429-chr4:57298915..57301727,2	K562	blood:
6	chr4:57250870..57256080-chr4:57298204..57304153,16	K562	blood:
7	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
8	chr4:57300392..57305074-chr4:57333261..57337861,17	MCF-7	breast:
9	chr4:57275040..57277242-chr4:57300118..57301937,2	MCF-7	breast:
10	chr4:57299474..57303800-chr4:57395386..57399526,7	K562	blood:
11	chr4:57300865..57304829-chr4:57331110..57333239,4	MCF-7	breast:
12	chr4:57299951..57301849-chr4:57773604..57776000,3	K562	blood:
13	chr4:56813951..56816639-chr4:57299941..57302593,2	K562	blood:
14	chr4:57250870..57256510-chr4:57298204..57303491,14	K562	blood:
15	chr4:57251780..57255283-chr4:57300557..57304376,5	MCF-7	breast:

Variant related genes	Relation type
PAICS	TF binding region
ENSG00000174799	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000249693	Chromatin interaction
ENSG00000134852	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000272969	Chromatin interaction
ENSG00000268171	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000270109	Chromatin interaction
ENSG00000157426	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12503885	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12505749	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12511049	1.00[CEU][hapmap]
rs1520025	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086758	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17086939	0.89[JPT][hapmap]
rs17756240	0.85[AFR][1000 genomes]
rs4260596	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs4865086	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[ASN][1000 genomes]
rs55644848	0.85[AFR][1000 genomes]
rs60972582	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6834384	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6843073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7693436	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[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9799408	1.00[CHB][hapmap];0.90[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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7435941	SRP72	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:57295000-57305000	Active TSS	GM12878-XiMat	blood
4	chr4:57298400-57305600	Active TSS	Hela-S3	cervix
5	chr4:57299200-57302600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:57299200-57304000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:57299200-57304200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr4:57299200-57304400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:57299200-57304400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr4:57299200-57304800	Active TSS	H9 Cell Line	embryonic stem cell
11	chr4:57299200-57305000	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr4:57299200-57305800	Active TSS	H1 Cell Line	embryonic stem cell
13	chr4:57299200-57305800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr4:57299200-57305800	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr4:57299400-57301000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:57299400-57301200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:57299400-57301400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:57299400-57304200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr4:57299400-57304200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:57299400-57304400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:57299400-57304800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:57299400-57305000	Active TSS	K562	blood
23	chr4:57299600-57301000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr4:57299600-57304400	Active TSS	A549	lung
25	chr4:57299800-57301200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:57299800-57301600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:57299800-57303000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr4:57299800-57304400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:57299800-57304400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:57299800-57304400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:57299800-57304800	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr4:57299800-57305600	Active TSS	HepG2	liver
33	chr4:57300000-57304000	Active TSS	HSMM	muscle
34	chr4:57300000-57304400	Active TSS	Ovary	ovary
35	chr4:57300200-57301000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr4:57300200-57301000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr4:57300200-57304000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:57300200-57304000	Active TSS	NH-A	brain
39	chr4:57300400-57301000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:57300400-57301000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:57300400-57301000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr4:57300400-57301000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:57300400-57301000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr4:57300400-57301000	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr4:57300400-57301000	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr4:57300400-57301000	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr4:57300400-57301000	Flanking Active TSS	Fetal Brain Male	brain
48	chr4:57300400-57301400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:57300400-57301400	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr4:57300400-57301400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links