Variant report

Variant	rs35146811
Chromosome Location	chr7:99720994-99720995
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99720589-99726750	HepG2	liver:	n/a	n/a
2	STAT3	chr7:99720973-99721106	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99717030..99721378-chr7:100025256..100028946,7	MCF-7	breast:
2	chr7:99719960..99722243-chr7:99751979..99754422,2	MCF-7	breast:
3	chr7:99720230..99721942-chr7:99948309..99949979,2	MCF-7	breast:
4	chr7:99719816..99722577-chr7:99753597..99756581,3	K562	blood:
5	chr7:99709712..99711434-chr7:99720028..99722233,2	K562	blood:
6	chr7:99720651..99722811-chr7:99761432..99764330,2	K562	blood:
7	chr7:99719091..99721941-chr7:99753666..99756777,4	MCF-7	breast:

No data

Variant related genes	Relation type
TAF6	TF binding region
MBLAC1	TF binding region
ENSG00000272752	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000121716	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000266154	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10281368	0.84[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap]
rs1043915	0.83[CEU][hapmap]
rs1061230	0.83[CEU][hapmap]
rs11505847	0.82[AMR][1000 genomes]
rs11764176	0.83[CEU][hapmap]
rs11771139	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11771331	0.86[MEX][hapmap]
rs12666425	0.83[CEU][hapmap]
rs12705070	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs12705071	0.97[TSI][hapmap]
rs13223792	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.92[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]
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]
rs1880949	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]
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]
rs35991721	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3779045	0.83[CEU][hapmap]
rs4134903	0.84[ASW][hapmap];0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4424195	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs4729566	0.85[MEX][hapmap]
rs6948729	0.83[CEU][hapmap]
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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs35146811	GATS	cis	cerebellum	SCAN
rs35146811	GATS	cis	lymphoblastoid	seeQTL
rs35146811	ZKSCAN1	cis	cerebellum	SCAN
rs35146811	LRWD1	cis	parietal	SCAN
rs35146811	GATS	cis	parietal	SCAN
rs35146811	LRRC17	cis	parietal	SCAN
rs35146811	ZSCAN21	cis	parietal	SCAN
rs35146811	ZNF498	cis	cerebellum	SCAN
rs35146811	GAL3ST4	cis	cerebellum	SCAN
rs35146811	SHFM1	cis	parietal	SCAN
rs35146811	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs35146811	BUD31	cis	parietal	SCAN
rs35146811	PILRB	cis	parietal	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	chr7:99718400-99722000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:99718400-99722200	Weak transcription	Esophagus	oesophagus
7	chr7:99718400-99722400	Weak transcription	Pancreas	Pancrea
8	chr7:99718400-99722800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:99718400-99723800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:99718400-99723800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:99718400-99724000	Weak transcription	Left Ventricle	heart
12	chr7:99718600-99721800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:99718600-99721800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:99718600-99721800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr7:99718600-99721800	Weak transcription	Fetal Intestine Large	intestine
16	chr7:99718600-99721800	Weak transcription	GM12878-XiMat	blood
17	chr7:99718600-99721800	Weak transcription	NHLF	lung
18	chr7:99718600-99722000	Weak transcription	Primary B cells from cord blood	blood
19	chr7:99718600-99722000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:99718600-99722200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:99718600-99722400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:99718600-99722400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:99718600-99722600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:99718600-99722600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:99718600-99722600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr7:99718600-99722600	Weak transcription	Liver	Liver
27	chr7:99718600-99722600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr7:99718600-99723000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:99718600-99723200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:99718600-99723200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:99718600-99723800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:99718600-99723800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr7:99718600-99723800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:99718600-99723800	Weak transcription	Brain Angular Gyrus	brain
35	chr7:99718600-99723800	Weak transcription	Brain Anterior Caudate	brain
36	chr7:99718600-99723800	Weak transcription	HSMM	muscle
37	chr7:99718600-99723800	Weak transcription	HUVEC	blood vessel
38	chr7:99718600-99723800	Weak transcription	Osteobl	bone
39	chr7:99718600-99724000	Weak transcription	Brain Substantia Nigra	brain
40	chr7:99718600-99724000	Weak transcription	Fetal Kidney	kidney
41	chr7:99718600-99724000	Weak transcription	Right Atrium	heart
42	chr7:99718600-99724000	Weak transcription	HSMMtube	muscle
43	chr7:99718600-99724000	Weak transcription	NH-A	brain
44	chr7:99718600-99724000	Weak transcription	NHDF-Ad	bronchial
45	chr7:99718800-99723800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr7:99718800-99724000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr7:99719600-99722000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr7:99719600-99722200	Strong transcription	Fetal Muscle Leg	muscle
49	chr7:99719600-99723600	Strong transcription	Fetal Stomach	stomach
50	chr7:99719800-99721000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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