Variant report

Variant	rs798549
Chromosome Location	chr7:2760750-2760751
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:2751778..2761552-chr7:2768388..2775125,13	K562	blood:
2	chr7:2760607..2761112-chr7:2860852..2861356,2	MCF-7	breast:
3	chr7:2749908..2752648-chr7:2759444..2761951,3	MCF-7	breast:
4	chr7:2724386..2733394-chr7:2753206..2761980,25	MCF-7	breast:
5	chr7:2758129..2761976-chr7:2763173..2766287,3	MCF-7	breast:
6	chr7:2758388..2761774-chr7:2912256..2915270,3	K562	blood:
7	chr7:2760749..2763045-chr7:2764793..2766522,2	K562	blood:
8	chr7:2757306..2759067-chr7:2759260..2762192,2	K562	blood:
9	chr7:2760677..2762584-chr7:2771267..2773265,2	MCF-7	breast:
10	chr7:2758216..2760821-chr7:2762447..2764162,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000174945	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11765492	0.82[YRI][hapmap]
rs11772508	0.86[MKK][hapmap];0.82[YRI][hapmap]
rs208345	0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs208346	0.82[CHB][hapmap]
rs208352	0.90[ASN][1000 genomes]
rs208354	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs208356	0.82[CHB][hapmap]
rs2255541	0.81[CHB][hapmap]
rs2255782	0.81[CHB][hapmap]
rs2266925	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2527689	0.85[CHB][hapmap]
rs2644272	0.82[CHB][hapmap]
rs2644311	0.82[CHB][hapmap]
rs709280	0.85[CHB][hapmap]
rs798515	0.84[CHB][hapmap]
rs798517	0.86[CHB][hapmap]
rs798519	0.82[CHB][hapmap]
rs798521	0.82[CHB][hapmap]
rs798522	0.82[CHB][hapmap]
rs798525	0.82[CHB][hapmap]
rs798527	0.82[CHB][hapmap]
rs798530	0.81[CHB][hapmap]
rs798532	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798533	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798534	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs798535	0.97[ASN][1000 genomes]
rs798537	0.97[ASN][1000 genomes]
rs798538	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs798541	0.94[ASN][1000 genomes]
rs798542	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798543	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798553	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471227	chr7:2629020-2768864	Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv887309	chr7:2664214-2763102	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv887312	chr7:2707822-2763102	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1024023	chr7:2726210-2829581	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538653	chr7:2726210-2829581	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1017611	chr7:2750418-2781716	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv538654	chr7:2750418-2781716	Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv971480	chr7:2755767-2765866	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs798549	C7orf50	cis	parietal	SCAN
rs798549	GNA12	cis	brain	BrainEAC
rs798549	GET4	cis	parietal	SCAN
rs798549	INTS1	cis	parietal	SCAN
rs798549	GNA12	cis	hippocampus	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2742200-2765600	Weak transcription	HSMM	muscle
2	chr7:2749000-2760800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr7:2749400-2770600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:2749800-2770800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:2750000-2760800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:2750000-2762800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:2750000-2765600	Weak transcription	Brain Substantia Nigra	brain
8	chr7:2750000-2767800	Weak transcription	Osteobl	bone
9	chr7:2750000-2768400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:2750000-2769000	Weak transcription	NHDF-Ad	bronchial
11	chr7:2750200-2765800	Weak transcription	Liver	Liver
12	chr7:2751000-2764400	Weak transcription	Brain Germinal Matrix	brain
13	chr7:2751200-2768400	Weak transcription	Brain Angular Gyrus	brain
14	chr7:2752400-2796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:2753400-2765800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:2753600-2768800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:2754600-2766800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:2754800-2774200	Weak transcription	Fetal Brain Male	brain
19	chr7:2755800-2761400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:2755800-2770600	Weak transcription	Fetal Kidney	kidney
21	chr7:2756000-2777800	Weak transcription	Psoas Muscle	Psoas
22	chr7:2756200-2761200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr7:2756200-2762800	Weak transcription	HSMMtube	muscle
24	chr7:2756200-2770600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr7:2756400-2765600	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:2757200-2767400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:2757200-2770600	Weak transcription	Esophagus	oesophagus
28	chr7:2757400-2766200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:2757600-2772800	Weak transcription	Small Intestine	intestine
30	chr7:2757800-2761000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:2757800-2761200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:2757800-2761600	Weak transcription	Left Ventricle	heart
33	chr7:2757800-2763800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr7:2757800-2766800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:2757800-2768200	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:2757800-2768400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr7:2758000-2761600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:2758000-2764600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr7:2758000-2765600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:2758000-2765800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:2758000-2768400	Weak transcription	HepG2	liver
42	chr7:2758000-2768600	Weak transcription	Right Atrium	heart
43	chr7:2758200-2762800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr7:2758200-2762800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:2758200-2762800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr7:2758200-2765400	Weak transcription	Colonic Mucosa	Colon
47	chr7:2758200-2766000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr7:2758200-2768000	Strong transcription	Fetal Stomach	stomach
49	chr7:2758200-2769400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr7:2758400-2762800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links