Variant report

Variant	rs72800543
Chromosome Location	chr2:46774479-46774480
allele	A/G
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	NFIC	chr2:46774317-46774766	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:46774348-46775038	GM12878	blood:	n/a	n/a
3	RXRA	chr2:46774232-46774784	HepG2	liver:	n/a	chr2:46774518-46774527 chr2:46774519-46774532 chr2:46774519-46774532 chr2:46774515-46774535 chr2:46774519-46774532 chr2:46774519-46774533 chr2:46774517-46774533
4	CTCF	chr2:46774408-46774499	GM12878	blood:	n/a	n/a
5	HNF4G	chr2:46774265-46774778	HepG2	liver:	n/a	chr2:46774551-46774563 chr2:46774519-46774532 chr2:46774518-46774532 chr2:46774519-46774531 chr2:46774519-46774531 chr2:46774516-46774534 chr2:46774519-46774531 chr2:46774514-46774536 chr2:46774518-46774530 chr2:46774518-46774531 chr2:46774519-46774532 chr2:46774519-46774532 chr2:46774518-46774532 chr2:46774519-46774531 chr2:46774518-46774533 chr2:46774518-46774532
6	MYBL2	chr2:46774109-46774825	HepG2	liver:	n/a	n/a
7	RFX5	chr2:46774358-46774672	HepG2	liver:	n/a	n/a
8	MYBL2	chr2:46774164-46774795	HepG2	liver:	n/a	n/a
9	CHD2	chr2:46774401-46774618	HepG2	liver:	n/a	n/a
10	SPI1	chr2:46774442-46774879	GM12891	blood:	n/a	n/a
11	BHLHE40	chr2:46774404-46774844	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:46770477-46777171	GM12878	blood:	n/a	n/a
13	REST	chr2:46774280-46774685	HepG2	liver:	n/a	n/a
14	RELA	chr2:46774415-46775849	GM19099	blood:	n/a	n/a
15	TCF12	chr2:46774240-46774810	HepG2	liver:	n/a	n/a
16	TEAD4	chr2:46774228-46774785	HepG2	liver:	n/a	n/a
17	NFIC	chr2:46774286-46774832	HepG2	liver:	n/a	n/a
18	CHD1	chr2:46774476-46774632	GM12878	blood:	n/a	n/a
19	EP300	chr2:46774278-46774771	HepG2	liver:	n/a	n/a
20	NR2F2	chr2:46774152-46774921	HepG2	liver:	n/a	chr2:46774515-46774530 chr2:46774551-46774566
21	BHLHE40	chr2:46774379-46774786	HepG2	liver:	n/a	n/a
22	BATF	chr2:46774396-46774823	GM12878	blood:	n/a	n/a
23	NR2F2	chr2:46774069-46774966	HepG2	liver:	n/a	chr2:46774515-46774530 chr2:46774551-46774566
24	HNF4A	chr2:46774410-46774760	HepG2	liver:	n/a	chr2:46774551-46774563 chr2:46774519-46774532 chr2:46774518-46774532 chr2:46774519-46774531 chr2:46774519-46774531 chr2:46774516-46774534 chr2:46774519-46774531 chr2:46774514-46774536 chr2:46774518-46774530 chr2:46774518-46774531 chr2:46774519-46774532 chr2:46774519-46774532 chr2:46774518-46774532 chr2:46774519-46774531 chr2:46774518-46774532
25	MAFF	chr2:46774377-46774641	HepG2	liver:	n/a	n/a
26	SRF	chr2:46774315-46774627	HepG2	liver:	n/a	chr2:46774473-46774490
27	IRF4	chr2:46774385-46774781	GM12878	blood:	n/a	n/a
28	RAD21	chr2:46774354-46774570	HepG2	liver:	n/a	n/a
29	RXRA	chr2:46774031-46774828	HepG2	liver:	n/a	chr2:46774518-46774527 chr2:46774112-46774132 chr2:46774519-46774532 chr2:46774519-46774532 chr2:46774189-46774198 chr2:46774515-46774535 chr2:46774519-46774532 chr2:46774519-46774533 chr2:46774517-46774533
30	RUNX3	chr2:46774458-46774853	GM12878	blood:	n/a	n/a
31	SP1	chr2:46774256-46774728	HepG2	liver:	n/a	n/a
32	MAFK	chr2:46774429-46774618	HepG2	liver:	n/a	n/a
33	SPI1	chr2:46774406-46775153	GM12878	blood:	n/a	n/a
34	WRNIP1	chr2:46774378-46774677	GM12878	blood:	n/a	n/a
35	EP300	chr2:46774317-46774822	HepG2	liver:	n/a	n/a
36	POLR2A	chr2:46774000-46774985	GM12878	blood:	n/a	n/a
37	HNF4A	chr2:46774363-46774789	HepG2	liver:	n/a	chr2:46774551-46774563 chr2:46774519-46774532 chr2:46774518-46774532 chr2:46774519-46774531 chr2:46774519-46774531 chr2:46774516-46774534 chr2:46774519-46774531 chr2:46774514-46774536 chr2:46774518-46774530 chr2:46774518-46774531 chr2:46774519-46774532 chr2:46774519-46774532 chr2:46774518-46774532 chr2:46774519-46774531 chr2:46774518-46774532
38	POLR2A	chr2:46773994-46777188	GM12878	blood:	n/a	n/a
39	HDAC2	chr2:46774342-46774820	HepG2	liver:	n/a	n/a
40	RCOR1	chr2:46774356-46774695	HepG2	liver:	n/a	n/a
41	BHLHE40	chr2:46774377-46774697	HepG2	liver:	n/a	n/a
42	SRF	chr2:46774345-46774662	HepG2	liver:	n/a	chr2:46774473-46774490
43	ARID3A	chr2:46774431-46774676	HepG2	liver:	n/a	n/a
44	CTCF	chr2:46774440-46774590	GM12864	blood:	n/a	n/a
45	FOXA1	chr2:46774261-46774748	HepG2	liver:	n/a	n/a
46	MYC	chr2:46774412-46774688	HepG2	liver:	n/a	n/a
47	HNF4A	chr2:46774365-46774717	HepG2	liver:	n/a	chr2:46774551-46774563 chr2:46774519-46774532 chr2:46774518-46774532 chr2:46774519-46774531 chr2:46774519-46774531 chr2:46774516-46774534 chr2:46774519-46774531 chr2:46774514-46774536 chr2:46774518-46774530 chr2:46774518-46774531 chr2:46774519-46774532 chr2:46774519-46774532 chr2:46774518-46774532 chr2:46774519-46774531 chr2:46774518-46774532
48	JUND	chr2:46774415-46774701	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:46774212..46777440-chr2:46842823..46846024,3	K562	blood:
2	chr2:46773314..46775192-chr2:47402106..47404566,2	K562	blood:
3	chr2:46769021..46773979-chr2:46774333..46777688,7	MCF-7	breast:
4	chr2:46773973..46776728-chr2:46790942..46793307,2	MCF-7	breast:
5	chr2:46721184..46729524-chr2:46766976..46775977,14	K562	blood:

Variant related genes	Relation type
ATP6V1E2	TF binding region
ENSG00000119729	Chromatin interaction
ENSG00000119878	Chromatin interaction
ENSG00000250565	Chromatin interaction
ENSG00000253515	Chromatin interaction
ENSG00000151665	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17767307	1.00[AFR][1000 genomes]
rs17771017	1.00[AFR][1000 genomes]
rs17821989	1.00[AFR][1000 genomes]
rs41371146	1.00[AFR][1000 genomes]
rs41379148	1.00[AFR][1000 genomes]
rs56006635	1.00[AFR][1000 genomes]
rs56224128	1.00[AFR][1000 genomes]
rs72800535	1.00[AFR][1000 genomes]
rs72800550	1.00[AFR][1000 genomes]
rs72802415	1.00[AFR][1000 genomes]
rs72802420	1.00[AFR][1000 genomes]
rs72802426	1.00[AFR][1000 genomes]
rs72802429	1.00[AFR][1000 genomes]
rs72802430	1.00[AFR][1000 genomes]
rs72802435	1.00[AFR][1000 genomes]
rs72802444	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72800543	FLJ41757	cis	brain	BrainEAC

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771000-46776600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr2:46771000-46781600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:46771200-46774600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:46771200-46774800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:46771200-46778000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:46771200-46780000	Enhancers	Psoas Muscle	Psoas
7	chr2:46771200-46781400	Weak transcription	NHEK	skin
8	chr2:46771200-46781600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:46771200-46781600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:46771400-46774800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr2:46771400-46777000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:46771400-46778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:46771400-46780000	Genic enhancers	Fetal Muscle Leg	muscle
15	chr2:46771400-46781600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:46771400-46789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:46771400-46796000	Weak transcription	Fetal Kidney	kidney
18	chr2:46771600-46774600	Weak transcription	Fetal Brain Female	brain
19	chr2:46771600-46777000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:46771600-46781600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:46771600-46781600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:46771800-46774800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:46771800-46775400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:46771800-46777000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:46771800-46777000	Enhancers	Brain Angular Gyrus	brain
26	chr2:46771800-46777600	Enhancers	Brain Cingulate Gyrus	brain
27	chr2:46771800-46780000	Enhancers	Right Atrium	heart
28	chr2:46771800-46781400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:46771800-46781400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:46771800-46781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:46771800-46782000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:46771800-46782400	Weak transcription	HMEC	breast
33	chr2:46771800-46795600	Weak transcription	Fetal Brain Male	brain
34	chr2:46772000-46774600	Weak transcription	Fetal Intestine Small	intestine
35	chr2:46772000-46777200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:46772000-46782600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:46772200-46776000	Enhancers	Primary hematopoietic stem cells	blood
38	chr2:46772200-46776200	Enhancers	Colon Smooth Muscle	Colon
39	chr2:46772200-46780200	Genic enhancers	Left Ventricle	heart
40	chr2:46772200-46804000	Weak transcription	NH-A	brain
41	chr2:46772400-46774600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:46772400-46775000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:46772400-46775200	Strong transcription	A549	lung
44	chr2:46772400-46775400	Weak transcription	Dnd41	blood
45	chr2:46772400-46777000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:46772400-46777000	Genic enhancers	NHDF-Ad	bronchial
47	chr2:46772800-46774600	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr2:46772800-46776000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
49	chr2:46772800-46776200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:46772800-46777600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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