Variant report

Variant	rs7949349
Chromosome Location	chr11:9200299-9200300
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	chr11:9169410..9173680-chr11:9196051..9200398,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184014	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10454487	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840170	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs10840186	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10840188	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840189	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042196	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[EUR][1000 genomes]
rs11042197	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11042201	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11042215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042217	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11042224	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042228	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042230	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042231	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042232	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042233	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042240	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042241	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042242	1.00[ASN][1000 genomes]
rs11042246	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042253	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042257	0.85[EUR][1000 genomes]
rs11042259	0.85[EUR][1000 genomes]
rs11042268	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1136966	1.00[CHB][hapmap]
rs11607384	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs11827186	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12286621	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360767	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362997	0.85[EUR][1000 genomes]
rs12363839	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17257379	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984775	1.00[CHB][hapmap]
rs2133215	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173406	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4061640	1.00[CHB][hapmap]
rs4627079	0.85[EUR][1000 genomes]
rs4910443	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs4910446	0.85[EUR][1000 genomes]
rs55962227	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56294473	1.00[ASN][1000 genomes]
rs60693427	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6486138	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6486204	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486209	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66554737	1.00[ASN][1000 genomes]
rs7103472	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7113467	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs7114013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7115283	0.86[EUR][1000 genomes]
rs7121753	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129049	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130400	1.00[ASN][1000 genomes]
rs72857989	0.81[EUR][1000 genomes]
rs72857991	0.81[EUR][1000 genomes]
rs72857993	0.81[EUR][1000 genomes]
rs72857997	0.83[EUR][1000 genomes]
rs72859608	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72859676	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72859678	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72859693	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72861335	0.85[EUR][1000 genomes]
rs7394454	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7394869	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7395631	1.00[ASN][1000 genomes]
rs7396115	1.00[CHB][hapmap]
rs7396130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7396541	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7396840	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7929621	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7936201	1.00[CHB][hapmap]
rs7936622	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938562	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940872	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941341	1.00[CHB][hapmap]
rs7945570	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945759	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7949022	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs9645644	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7949349	OR10A6	cis	cerebellum	SCAN
rs7949349	OR56A1	cis	cerebellum	SCAN
rs7949349	TMEM41B	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9155000-9203400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:9161200-9202400	Weak transcription	Small Intestine	intestine
3	chr11:9162000-9230600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:9166000-9200600	Weak transcription	Colonic Mucosa	Colon
5	chr11:9169600-9238000	Weak transcription	Esophagus	oesophagus
6	chr11:9171800-9230200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:9172000-9230400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:9174000-9225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:9182400-9225000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:9182400-9231800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr11:9184200-9208200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:9184200-9216800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr11:9186800-9215800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:9187600-9201800	Weak transcription	Pancreas	Pancrea
15	chr11:9193800-9202600	Weak transcription	Fetal Heart	heart
16	chr11:9194000-9203400	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr11:9196200-9200400	Strong transcription	HUVEC	blood vessel
18	chr11:9196200-9203800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr11:9196400-9203200	Strong transcription	NHLF	lung
20	chr11:9196400-9204000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:9196600-9203000	Strong transcription	HSMM	muscle
22	chr11:9196800-9208200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:9197000-9202800	Strong transcription	Fetal Kidney	kidney
24	chr11:9197000-9203000	Strong transcription	Primary B cells from cord blood	blood
25	chr11:9197000-9203000	Strong transcription	NH-A	brain
26	chr11:9197000-9203200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr11:9197000-9203200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr11:9197000-9203800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:9197000-9205400	Strong transcription	Primary hematopoietic stem cells	blood
30	chr11:9197000-9210600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:9197200-9201000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:9197200-9202800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr11:9197200-9202800	Strong transcription	Liver	Liver
34	chr11:9197200-9203600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr11:9197400-9203000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr11:9197400-9203400	Strong transcription	Primary T cells from cord blood	blood
37	chr11:9197600-9200400	Strong transcription	Brain Anterior Caudate	brain
38	chr11:9197600-9200600	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr11:9197600-9200600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:9197600-9200800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:9197600-9200800	Strong transcription	Fetal Intestine Large	intestine
42	chr11:9197600-9202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:9197600-9202200	Strong transcription	Adipose Nuclei	Adipose
44	chr11:9197600-9202400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:9197600-9202400	Strong transcription	Fetal Thymus	thymus
46	chr11:9197600-9202400	Strong transcription	Left Ventricle	heart
47	chr11:9197600-9202400	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:9197600-9202600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr11:9197600-9202600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:9197600-9203000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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