Variant report

Variant	rs7108907
Chromosome Location	chr11:9871113-9871114
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	chr11:9868824..9871415-chr11:9878281..9879857,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10770068	1.00[JPT][hapmap]
rs10840311	0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12574461	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12574467	0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12574474	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12574508	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12574765	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12576762	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12576763	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12577960	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12578023	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12786236	1.00[YRI][hapmap]
rs17268414	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2403221	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2403222	1.00[JPT][hapmap]
rs360118	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7951573	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs958875	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7108907	SNORA23	cis	cerebellum	SCAN
rs7108907	EIF4G2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9818600-9881400	Weak transcription	Spleen	Spleen
2	chr11:9830400-9880400	Weak transcription	Thymus	Thymus
3	chr11:9830800-9880600	Weak transcription	Fetal Brain Male	brain
4	chr11:9833600-9878800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:9834200-9876600	Weak transcription	Brain Germinal Matrix	brain
6	chr11:9834600-9877200	Weak transcription	Right Ventricle	heart
7	chr11:9837600-9885800	Weak transcription	Hela-S3	cervix
8	chr11:9838600-9879800	Weak transcription	Fetal Thymus	thymus
9	chr11:9848200-9877000	Weak transcription	HepG2	liver
10	chr11:9851200-9880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:9851600-9875400	Weak transcription	Stomach Mucosa	stomach
12	chr11:9851600-9880400	Weak transcription	Small Intestine	intestine
13	chr11:9853000-9871600	Weak transcription	Fetal Intestine Small	intestine
14	chr11:9853400-9877400	Weak transcription	Brain Substantia Nigra	brain
15	chr11:9854000-9877400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:9854000-9880600	Weak transcription	Colonic Mucosa	Colon
17	chr11:9856600-9880000	Weak transcription	Fetal Heart	heart
18	chr11:9859000-9872800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:9859600-9871400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:9859800-9880200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr11:9861400-9872600	Weak transcription	HUVEC	blood vessel
22	chr11:9861400-9874000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:9861400-9875400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:9861400-9877000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:9861400-9877400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:9861400-9879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:9861400-9879800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:9861400-9879800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:9861400-9880800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr11:9862600-9873200	Strong transcription	Fetal Intestine Large	intestine
31	chr11:9863000-9871200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr11:9863000-9879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:9863200-9876800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:9863400-9876000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr11:9863400-9877600	Weak transcription	HMEC	breast
36	chr11:9863400-9880000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:9863600-9879800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:9863800-9883800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:9864000-9875400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr11:9864800-9871600	Weak transcription	Fetal Stomach	stomach
41	chr11:9865000-9879800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:9865800-9877200	Weak transcription	Gastric	stomach
43	chr11:9866000-9880400	Weak transcription	Esophagus	oesophagus
44	chr11:9866000-9880400	Weak transcription	Pancreas	Pancrea
45	chr11:9866600-9872200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:9866800-9871800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:9868400-9872800	Weak transcription	NH-A	brain
48	chr11:9868400-9877200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr11:9868600-9873200	Weak transcription	A549	lung
50	chr11:9868600-9876800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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