Variant report

Variant	rs6978094
Chromosome Location	chr7:21954865-21954866
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:21877891..21879922-chr7:21953587..21955400,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10950883	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1128250	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12055905	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12055908	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12539984	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12673256	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12700327	0.83[ASW][hapmap]
rs1919906	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4394298	0.81[TSI][hapmap]
rs4566940	0.83[ASW][hapmap]
rs55658106	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57033293	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57082026	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59258063	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62445924	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62445926	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62445928	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62445933	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6946675	0.81[TSI][hapmap]
rs6959493	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6959806	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6963571	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7798564	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs7807924	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1027453	chr7:21918474-21982448	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6978094	C7orf46	cis	parietal	SCAN
rs6978094	IL6	cis	cerebellum	SCAN
rs6978094	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21933000-21963200	Weak transcription	A549	lung
2	chr7:21936600-21956400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr7:21936600-21956600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:21937000-21956400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:21937200-21956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:21937400-21956000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:21937600-21956200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:21937600-21956400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:21937800-21956000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr7:21937800-21956200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:21938000-21955000	Weak transcription	Stomach Mucosa	stomach
12	chr7:21938000-21956200	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr7:21938600-21984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:21938800-21956600	Strong transcription	Primary T cells from cord blood	blood
15	chr7:21942000-21955400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:21942400-21957200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:21943000-21955000	Weak transcription	Fetal Kidney	kidney
18	chr7:21944000-21957400	Weak transcription	Colonic Mucosa	Colon
19	chr7:21944200-21956200	Weak transcription	Spleen	Spleen
20	chr7:21944400-21956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:21946000-21956200	Weak transcription	Brain Substantia Nigra	brain
22	chr7:21946000-21956400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr7:21946200-21955600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:21946200-21957600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr7:21946200-21963400	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:21947800-21956000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:21947800-21958000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:21948200-21956400	Weak transcription	Fetal Intestine Large	intestine
29	chr7:21948400-21956400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:21948400-21960400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr7:21948800-21981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr7:21949800-21955800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:21950400-21960400	Weak transcription	Fetal Brain Female	brain
34	chr7:21950800-21956600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:21951400-21955800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr7:21951600-21955200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr7:21951600-21982600	Weak transcription	HSMM	muscle
38	chr7:21951800-21955000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:21952000-21955000	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr7:21952000-21956200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr7:21952400-21956200	Strong transcription	Fetal Stomach	stomach
42	chr7:21952400-21963200	Weak transcription	Psoas Muscle	Psoas
43	chr7:21952600-21958400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr7:21952600-21977400	Weak transcription	NHDF-Ad	bronchial
45	chr7:21952800-21955000	Strong transcription	Fetal Intestine Small	intestine
46	chr7:21952800-21955000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr7:21952800-21955000	Strong transcription	GM12878-XiMat	blood
48	chr7:21952800-21955600	Weak transcription	Adipose Nuclei	Adipose
49	chr7:21952800-21955800	Weak transcription	Osteobl	bone
50	chr7:21952800-21956000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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