Variant report

Variant	rs1880949
Chromosome Location	chr7:99722266-99722267
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99722218-99723396	K562	blood:	n/a	n/a
2	POLR2A	chr7:99722222-99722816	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:99722160-99723080	K562	blood:	n/a	n/a
4	ZNF263	chr7:99722166-99722735	HEK293-T-REx	kidney:	n/a	chr7:99722426-99722447
5	POLR2A	chr7:99722086-99722878	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr7:99722202-99722765	HCT-116	colon:	n/a	n/a
7	HDAC2	chr7:99722220-99722822	K562	blood:	n/a	n/a
8	POLR2A	chr7:99722254-99723045	K562	blood:	n/a	n/a
9	POLR2A	chr7:99721991-99723084	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr7:99721769-99723042	HepG2	liver:	n/a	n/a
11	POLR2A	chr7:99720589-99726750	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:99722141-99723257	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99722088..99724453-chr7:100026043..100027872,2	K562	blood:
2	chr7:99719816..99722577-chr7:99753597..99756581,3	K562	blood:
3	chr6:27834624..27836124-chr7:99722099..99724739,2	MCF-7	breast:
4	chr7:99720651..99722811-chr7:99761432..99764330,2	K562	blood:
5	chr7:99721104..99723072-chr7:99794545..99797155,2	MCF-7	breast:

No data

Variant related genes	Relation type
MBLAC1	TF binding region
TAF6	TF binding region
ENSG00000066923	Chromatin interaction
ENSG00000266154	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000184357	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10281368	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes]
rs1043915	0.83[CEU][hapmap]
rs1060544	0.80[AMR][1000 genomes]
rs1061230	0.83[CEU][hapmap]
rs11505847	0.83[AMR][1000 genomes]
rs11764176	0.83[CEU][hapmap]
rs11771139	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.91[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11771331	0.86[MEX][hapmap]
rs12666425	0.83[CEU][hapmap]
rs12705070	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs12705071	0.97[TSI][hapmap]
rs13223792	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap]
rs13230744	0.81[CEU][hapmap]
rs1527423	0.91[YRI][hapmap]
rs1534310	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1623264	0.83[CEU][hapmap]
rs1636975	0.83[CEU][hapmap]
rs1637001	0.83[CEU][hapmap]
rs1727133	0.83[CEU][hapmap]
rs1727134	0.83[CEU][hapmap]
rs1727138	0.83[CEU][hapmap]
rs1727140	0.83[CEU][hapmap]
rs2070215	0.97[TSI][hapmap]
rs2141160	0.81[CEU][hapmap]
rs2272345	0.83[CEU][hapmap]
rs2293479	0.82[CEU][hapmap];0.91[YRI][hapmap]
rs2528900	0.83[CEU][hapmap]
rs2950520	0.82[ASW][hapmap];0.83[CEU][hapmap]
rs35146811	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35991721	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3779045	0.83[CEU][hapmap]
rs4134903	0.84[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4424195	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs4729566	0.85[MEX][hapmap]
rs6948729	0.83[CEU][hapmap]
rs6953441	0.80[AMR][1000 genomes]
rs7788746	0.86[MEX][hapmap]
rs7794170	0.83[CEU][hapmap]
rs7811662	0.83[CEU][hapmap]
rs858506	0.83[CEU][hapmap]
rs866500	0.83[CEU][hapmap]
rs999885	0.95[YRI][hapmap]

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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers 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 miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs1880949	BUD31	cis	parietal	SCAN
rs1880949	TTLL1	trans	brain	seeQTL
rs1880949	SHFM1	cis	parietal	SCAN
rs1880949	ZKSCAN1	cis	multi-tissue	Pritchard
rs1880949	PILRB	cis	multi-tissue	Pritchard
rs1880949	GATS	cis	parietal	SCAN
rs1880949	GATS	cis	lymphoblastoid	seeQTL
rs1880949	GATS	cis	cerebellum	SCAN
rs1880949	B3GALT6	trans	brain	seeQTL
rs1880949	ZSCAN21	cis	parietal	SCAN
rs1880949	PILRB	cis	parietal	SCAN
rs1880949	GAL3ST4	cis	cerebellum	SCAN
rs1880949	Contig1998_RC	cis	multi-tissue	Pritchard
rs1880949	LRWD1	cis	parietal	SCAN
rs1880949	TRIM4	cis	multi-tissue	Pritchard
rs1880949	ZNF498	cis	cerebellum	SCAN
rs1880949	GATS	cis	multi-tissue	Pritchard
rs1880949	ZSCAN21	cis	Liver	GTEx
rs1880949	ZKSCAN1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99718200-99724000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:99718200-99724000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:99718200-99724000	Weak transcription	Ovary	ovary
4	chr7:99718200-99724000	Weak transcription	Psoas Muscle	Psoas
5	chr7:99718400-99722400	Weak transcription	Pancreas	Pancrea
6	chr7:99718400-99722800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:99718400-99723800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:99718400-99723800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr7:99718400-99724000	Weak transcription	Left Ventricle	heart
10	chr7:99718600-99722400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr7:99718600-99722400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr7:99718600-99722600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:99718600-99722600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr7:99718600-99722600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr7:99718600-99722600	Weak transcription	Liver	Liver
16	chr7:99718600-99722600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr7:99718600-99723000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:99718600-99723200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:99718600-99723200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:99718600-99723800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:99718600-99723800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:99718600-99723800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:99718600-99723800	Weak transcription	Brain Angular Gyrus	brain
24	chr7:99718600-99723800	Weak transcription	Brain Anterior Caudate	brain
25	chr7:99718600-99723800	Weak transcription	HSMM	muscle
26	chr7:99718600-99723800	Weak transcription	HUVEC	blood vessel
27	chr7:99718600-99723800	Weak transcription	Osteobl	bone
28	chr7:99718600-99724000	Weak transcription	Brain Substantia Nigra	brain
29	chr7:99718600-99724000	Weak transcription	Fetal Kidney	kidney
30	chr7:99718600-99724000	Weak transcription	Right Atrium	heart
31	chr7:99718600-99724000	Weak transcription	HSMMtube	muscle
32	chr7:99718600-99724000	Weak transcription	NH-A	brain
33	chr7:99718600-99724000	Weak transcription	NHDF-Ad	bronchial
34	chr7:99718800-99723800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr7:99718800-99724000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr7:99719600-99723600	Strong transcription	Fetal Stomach	stomach
37	chr7:99719800-99722400	Strong transcription	Thymus	Thymus
38	chr7:99719800-99723200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:99719800-99723400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr7:99720000-99723400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:99720000-99724000	Weak transcription	Fetal Brain Male	brain
42	chr7:99720200-99722400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:99720200-99722400	Weak transcription	NHEK	skin
44	chr7:99720200-99722800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr7:99720200-99722800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:99720400-99722400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:99720400-99722400	Strong transcription	Dnd41	blood
48	chr7:99720400-99722800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr7:99720400-99723200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr7:99720400-99723800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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