Variant report

Variant	rs6948096
Chromosome Location	chr7:117826664-117826665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:117825039..117827152-chr7:120589846..120592123,2	MCF-7	breast:
2	chr7:117825257..117827852-chr7:118309009..118311377,2	K562	blood:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10085904	0.93[EUR][1000 genomes]
rs10226152	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10227326	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10229589	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10241875	0.89[EUR][1000 genomes]
rs10252627	0.88[EUR][1000 genomes]
rs10267938	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10487390	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061731	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10953864	0.94[EUR][1000 genomes]
rs1117254	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11486992	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11543742	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11770353	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11979012	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12112697	0.82[EUR][1000 genomes]
rs12537795	0.94[EUR][1000 genomes]
rs12667103	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12673046	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13224733	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2041527	0.81[EUR][1000 genomes]
rs2041528	0.81[EUR][1000 genomes]
rs2058416	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2058417	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2191920	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2402322	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2896242	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802012	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141028	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41900	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41901	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41902	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41905	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41906	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41909	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41910	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41911	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41915	0.90[EUR][1000 genomes]
rs41916	0.90[EUR][1000 genomes]
rs41926	0.90[EUR][1000 genomes]
rs41933	0.88[EUR][1000 genomes]
rs41934	0.90[EUR][1000 genomes]
rs41935	0.90[EUR][1000 genomes]
rs41938	0.90[EUR][1000 genomes]
rs41939	0.90[EUR][1000 genomes]
rs41945	0.80[EUR][1000 genomes]
rs41960	0.84[EUR][1000 genomes]
rs5002233	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466650	0.84[EUR][1000 genomes]
rs6944524	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6946855	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6956486	0.94[EUR][1000 genomes]
rs6964911	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6965144	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779933	0.93[EUR][1000 genomes]
rs7796145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7796148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7797855	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7799229	0.92[EUR][1000 genomes]
rs7806490	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917761	0.91[EUR][1000 genomes]
rs9655829	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656260	0.94[EUR][1000 genomes]
rs979652	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9886333	0.82[EUR][1000 genomes]
rs989899	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6948096	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117823400-117826800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:117824800-117829000	Weak transcription	Lung	lung
3	chr7:117824800-117829200	Weak transcription	Gastric	stomach
4	chr7:117824800-117832600	Weak transcription	Pancreas	Pancrea
5	chr7:117825000-117827000	Weak transcription	Placenta	Placenta
6	chr7:117825000-117827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:117825000-117830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:117825000-117834000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:117825000-117842200	Weak transcription	Aorta	Aorta
10	chr7:117825200-117826800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:117825200-117826800	Enhancers	Colon Smooth Muscle	Colon
12	chr7:117825200-117826800	Enhancers	Fetal Heart	heart
13	chr7:117825200-117827000	Enhancers	Primary B cells from cord blood	blood
14	chr7:117825200-117827000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:117825200-117828000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr7:117825200-117828400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr7:117825200-117830600	Weak transcription	HSMMtube	muscle
18	chr7:117825200-117834000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr7:117825400-117826800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:117825400-117827200	Transcr. at gene 5' and 3'	Dnd41	blood
21	chr7:117825400-117827800	Enhancers	Primary T cells from cord blood	blood
22	chr7:117825400-117828000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr7:117825600-117826800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
24	chr7:117825600-117826800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr7:117825600-117826800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:117825600-117826800	Enhancers	Osteobl	bone
27	chr7:117825600-117827000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:117825600-117827000	Enhancers	Fetal Lung	lung
29	chr7:117825600-117827000	Genic enhancers	HSMM	muscle
30	chr7:117825600-117827400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:117825600-117827400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:117825600-117827400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:117825600-117827400	Weak transcription	Fetal Thymus	thymus
34	chr7:117825600-117827600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr7:117825600-117827600	Weak transcription	Fetal Muscle Leg	muscle
36	chr7:117825600-117828200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:117825600-117828400	Weak transcription	Colonic Mucosa	Colon
38	chr7:117825600-117829000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:117825600-117829000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:117825600-117829000	Weak transcription	Esophagus	oesophagus
41	chr7:117825600-117832000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr7:117825600-117834000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr7:117825600-117835000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:117825600-117835600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:117825600-117837200	Weak transcription	Left Ventricle	heart
46	chr7:117825800-117826800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr7:117825800-117826800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:117825800-117826800	Enhancers	NH-A	brain
49	chr7:117825800-117827200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr7:117825800-117827400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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