Variant report

Variant	rs10238003
Chromosome Location	chr7:8063796-8063797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:8063593..8066315-chr7:8067381..8070107,2	MCF-7	breast:
2	chr7:8062440..8065234-chr7:8085232..8088218,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10226865	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10253861	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10264999	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10278726	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10278791	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10281919	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11981372	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1476823	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs258850	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs258851	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs258852	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37976	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs37979	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs37982	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs37986	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs37987	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs37997	0.83[EUR][1000 genomes]
rs38000	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38007	0.81[EUR][1000 genomes]
rs38008	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38009	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38015	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4725055	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4725056	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4725059	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6463753	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6953808	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7796831	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7808399	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7810540	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9655516	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv518779	chr7:8055664-8077359	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10238003	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8036400-8077400	Weak transcription	Right Ventricle	heart
2	chr7:8036600-8064400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:8036600-8064400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:8036600-8074600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:8038000-8066000	Weak transcription	Pancreas	Pancrea
6	chr7:8038400-8066000	Weak transcription	Spleen	Spleen
7	chr7:8041600-8064400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:8041600-8095000	Weak transcription	Gastric	stomach
9	chr7:8041800-8075400	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:8042800-8064400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:8043000-8099200	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:8043600-8068400	Weak transcription	NH-A	brain
13	chr7:8043800-8064400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:8043800-8064600	Weak transcription	Small Intestine	intestine
15	chr7:8044200-8063800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:8044200-8066000	Weak transcription	Lung	lung
17	chr7:8044600-8074400	Weak transcription	Brain Angular Gyrus	brain
18	chr7:8044800-8064400	Weak transcription	Aorta	Aorta
19	chr7:8045200-8066000	Weak transcription	Fetal Brain Male	brain
20	chr7:8046800-8064200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:8046800-8064400	Weak transcription	Ovary	ovary
22	chr7:8046800-8066000	Weak transcription	Left Ventricle	heart
23	chr7:8046800-8074400	Weak transcription	Brain Substantia Nigra	brain
24	chr7:8047000-8064000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr7:8047000-8066000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr7:8047200-8063800	Weak transcription	Fetal Lung	lung
27	chr7:8047200-8064000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:8047200-8064000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr7:8047200-8064000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:8047200-8064400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr7:8047200-8065200	Weak transcription	Fetal Kidney	kidney
32	chr7:8047200-8065400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:8047200-8066000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr7:8047200-8066200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:8047400-8064000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:8047400-8064400	Weak transcription	Fetal Brain Female	brain
37	chr7:8047400-8064400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr7:8047400-8066000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr7:8047400-8066000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:8047400-8066000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr7:8047400-8075600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:8047600-8064400	Weak transcription	Fetal Muscle Leg	muscle
43	chr7:8047600-8108200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:8048200-8064400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:8048200-8064400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:8048400-8064200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr7:8048400-8064400	Weak transcription	Osteobl	bone
48	chr7:8049200-8066000	Weak transcription	Fetal Heart	heart
49	chr7:8051000-8064200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:8054800-8064200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links