Variant report

Variant	rs2896242
Chromosome Location	chr7:117824239-117824240
allele	C/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:39677208..39679664-chr7:117824087..117825656,2	MCF-7	breast:
2	chr14:70233418..70234082-chr7:117823597..117824354,2	Hela-S3	cervix:
3	chr20:30192446..30193095-chr7:117823800..117824567,2	Hela-S3	cervix:
4	chr3:64004028..64006157-chr7:117822623..117824945,2	MCF-7	breast:
5	chr7:117823617..117824609-chrX:53449148..53449800,2	Hela-S3	cervix:
6	chr7:117822159..117825807-chr7:117854196..117858736,4	K562	blood:
7	chr2:234775602..234777791-chr7:117824084..117825749,2	MCF-7	breast:
8	chr19:18303831..18304563-chr7:117823865..117824765,2	Hela-S3	cervix:
9	chr7:43965678..43966262-chr7:117823857..117824644,2	NB4	blood:

No data

Variant related genes	Relation type
ENSG00000254858	Chromatin interaction
ENSG00000078967	Chromatin interaction
ENSG00000100650	Chromatin interaction
ENSG00000224287	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000072501	Chromatin interaction
ENSG00000106608	Chromatin interaction
ENSG00000171346	Chromatin interaction
ENSG00000272181	Chromatin interaction
ENSG00000158423	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000106013	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	0.87[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes]
rs10226152	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10227326	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10229589	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10241875	0.89[EUR][1000 genomes]
rs10252627	0.88[EUR][1000 genomes]
rs10267938	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10487390	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054032	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061731	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10953864	0.94[EUR][1000 genomes]
rs1117254	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11486992	0.96[CEU][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11543742	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11770353	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11979012	0.95[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12112697	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12537795	0.88[CEU][hapmap];0.80[CHB][hapmap];0.94[EUR][1000 genomes]
rs12667103	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12673046	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13224733	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2041527	0.81[EUR][1000 genomes]
rs2041528	0.81[EUR][1000 genomes]
rs2058416	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2058417	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2191920	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2402322	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802012	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141028	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41900	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41901	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41902	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41905	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41906	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41909	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	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466650	0.84[EUR][1000 genomes]
rs6944524	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6946855	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6948096	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956486	0.94[EUR][1000 genomes]
rs6964911	0.87[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6965144	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779933	0.93[EUR][1000 genomes]
rs7796145	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7796148	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7797855	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7799229	0.88[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs7806490	0.91[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917761	0.91[EUR][1000 genomes]
rs9655829	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656260	0.94[EUR][1000 genomes]
rs979652	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9886333	0.82[EUR][1000 genomes]
rs989899	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
rs2896242	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117822400-117824800	Active TSS	Gastric	stomach
2	chr7:117822400-117825000	Active TSS	Fetal Intestine Large	intestine
3	chr7:117822400-117825600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr7:117822600-117825000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr7:117822600-117825800	Active TSS	Psoas Muscle	Psoas
6	chr7:117822800-117825200	Active TSS	Muscle Satellite Cultured Cells	--
7	chr7:117822800-117825200	Active TSS	GM12878-XiMat	blood
8	chr7:117822800-117825200	Active TSS	HMEC	breast
9	chr7:117822800-117825400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:117822800-117825600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:117822800-117825600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr7:117822800-117825600	Active TSS	A549	lung
13	chr7:117823000-117824600	Active TSS	Brain Angular Gyrus	brain
14	chr7:117823000-117824800	Active TSS	Brain Anterior Caudate	brain
15	chr7:117823000-117825200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:117823000-117825200	Active TSS	Colon Smooth Muscle	Colon
17	chr7:117823000-117825200	Active TSS	Fetal Muscle Leg	muscle
18	chr7:117823000-117825400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:117823000-117825400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:117823000-117825400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:117823000-117825400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:117823000-117825400	Active TSS	Colonic Mucosa	Colon
23	chr7:117823000-117825400	Active TSS	Thymus	Thymus
24	chr7:117823000-117825400	Active TSS	NHDF-Ad	bronchial
25	chr7:117823000-117825400	Active TSS	NHLF	lung
26	chr7:117823000-117825800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:117823000-117825800	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr7:117823000-117826000	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr7:117823000-117826000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:117823200-117824800	Active TSS	Esophagus	oesophagus
31	chr7:117823200-117824800	Active TSS	Left Ventricle	heart
32	chr7:117823200-117824800	Active TSS	Pancreas	Pancrea
33	chr7:117823200-117824800	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr7:117823200-117824800	Bivalent/Poised TSS	HepG2	liver
35	chr7:117823200-117825000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr7:117823200-117825000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:117823200-117825000	Active TSS	Aorta	Aorta
38	chr7:117823200-117825000	Active TSS	Fetal Kidney	kidney
39	chr7:117823200-117825000	Active TSS	Placenta Amnion	Placenta Amnion
40	chr7:117823200-117825000	Active TSS	Small Intestine	intestine
41	chr7:117823200-117825000	Active TSS	HSMM	muscle
42	chr7:117823200-117825200	Active TSS	H1 Cell Line	embryonic stem cell
43	chr7:117823200-117825200	Active TSS	H9 Cell Line	embryonic stem cell
44	chr7:117823200-117825200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:117823200-117825200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:117823200-117825200	Active TSS	Fetal Muscle Trunk	muscle
47	chr7:117823200-117825200	Active TSS	Stomach Mucosa	stomach
48	chr7:117823200-117825200	Active TSS	HSMMtube	muscle
49	chr7:117823200-117825400	Active TSS	Ovary	ovary
50	chr7:117823200-117825400	Active TSS	Right Ventricle	heart

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