Variant report

Variant	rs7800241
Chromosome Location	chr7:100468103-100468104
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	POLR2A	chr7:100468102-100468375	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:100467985-100468485	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:100468088-100468426	GM12892	blood:	n/a	n/a
4	POLR2A	chr7:100467859-100468865	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr7:100468043-100469471	K562	blood:	n/a	n/a
6	POLR2A	chr7:100467547-100468878	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr7:100468073-100468386	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr7:100467636-100468493	K562	blood:	n/a	n/a
9	POLR2A	chr7:100467670-100468710	K562	blood:	n/a	n/a
10	POLR2A	chr7:100468012-100468540	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr7:100467946-100468419	GM12878	blood:	n/a	n/a
12	POLR2A	chr7:100467710-100469443	K562	blood:	n/a	n/a
13	POLR2A	chr7:100467918-100468210	K562	blood:	n/a	n/a
14	POLR2A	chr7:100467723-100468378	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr7:100467997-100468501	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
SRRT	TF binding region
TRIP6	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12535629	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12538287	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075756	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808356	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3847067	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4727468	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6955197	0.93[ASN][1000 genomes]
rs7384255	0.92[ASN][1000 genomes]
rs7782299	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7784933	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7789085	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7794216	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS 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	90 gene(s)	inside rSNPs	diseases
7	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
9	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv888798	chr7:100406144-100472826	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	90 gene(s)	inside rSNPs	diseases
15	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
16	esv3382561	chr7:100466516-100468564	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7800241	TRRAP	cis	cerebellum	SCAN
rs7800241	FAM185A	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100461800-100471400	Weak transcription	HepG2	liver
2	chr7:100465600-100471800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr7:100465600-100471800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:100465600-100471800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr7:100465600-100472000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:100465800-100469400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:100465800-100472000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:100466000-100471600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr7:100466000-100471800	Weak transcription	Fetal Brain Male	brain
10	chr7:100466200-100468200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr7:100466200-100468400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:100466200-100468600	Weak transcription	Brain Anterior Caudate	brain
13	chr7:100466200-100468800	Weak transcription	Thymus	Thymus
14	chr7:100466200-100469000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:100466200-100471600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:100466200-100471600	Weak transcription	Brain Angular Gyrus	brain
17	chr7:100466200-100471600	Weak transcription	Brain Germinal Matrix	brain
18	chr7:100466200-100472000	Weak transcription	Fetal Kidney	kidney
19	chr7:100466400-100468200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:100466400-100468200	Weak transcription	Left Ventricle	heart
21	chr7:100466400-100468200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:100466400-100468400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:100466400-100468400	Weak transcription	A549	lung
24	chr7:100466400-100471600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr7:100466400-100471600	Weak transcription	Right Atrium	heart
26	chr7:100466400-100471800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr7:100466400-100471800	Weak transcription	Fetal Heart	heart
28	chr7:100466600-100468200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:100466600-100468200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:100466600-100471000	Strong transcription	Spleen	Spleen
31	chr7:100466600-100471400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr7:100466600-100471600	Weak transcription	Fetal Brain Female	brain
33	chr7:100466600-100471800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr7:100466600-100471800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr7:100466600-100471800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr7:100466600-100471800	Weak transcription	Primary B cells from cord blood	blood
37	chr7:100466600-100472000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:100466800-100468400	Weak transcription	Brain Substantia Nigra	brain
39	chr7:100466800-100469400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:100466800-100470000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr7:100466800-100471400	Weak transcription	Stomach Mucosa	stomach
42	chr7:100466800-100471600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr7:100466800-100471600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:100466800-100471800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:100467000-100468200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr7:100467000-100470000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr7:100467000-100470800	Weak transcription	GM12878-XiMat	blood
48	chr7:100467000-100471000	Strong transcription	NHEK	skin
49	chr7:100467000-100471400	Strong transcription	Fetal Intestine Small	intestine
50	chr7:100467000-100471400	Strong transcription	Fetal Muscle Leg	muscle

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