Variant report

Variant	rs11757098
Chromosome Location	chr6:49398861-49398862
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	chr6:49395795..49399005-chr6:49401983..49404851,4	K562	blood:

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10948498	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11752340	0.82[EUR][1000 genomes]
rs11752910	0.82[EUR][1000 genomes]
rs11755646	0.82[EUR][1000 genomes]
rs12173703	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12175251	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16879241	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs17805348	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1924982	0.86[EUR][1000 genomes]
rs2143730	0.82[EUR][1000 genomes]
rs28841337	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs471220	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs471316	0.85[EUR][1000 genomes]
rs471332	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs472313	0.83[EUR][1000 genomes]
rs474021	0.82[EUR][1000 genomes]
rs474897	0.83[EUR][1000 genomes]
rs475757	0.86[EUR][1000 genomes]
rs476131	0.80[CEU][hapmap]
rs478550	0.86[EUR][1000 genomes]
rs478991	0.83[CEU][hapmap]
rs481270	0.86[EUR][1000 genomes]
rs481959	0.81[EUR][1000 genomes]
rs482582	0.85[EUR][1000 genomes]
rs482930	0.84[EUR][1000 genomes]
rs483192	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs483827	0.81[EUR][1000 genomes]
rs484942	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs485383	0.86[EUR][1000 genomes]
rs485474	0.86[EUR][1000 genomes]
rs485772	0.86[EUR][1000 genomes]
rs485976	0.86[EUR][1000 genomes]
rs495303	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs495525	0.82[EUR][1000 genomes]
rs496864	0.86[EUR][1000 genomes]
rs498825	0.86[EUR][1000 genomes]
rs500811	0.84[EUR][1000 genomes]
rs501835	0.86[EUR][1000 genomes]
rs503680	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs510455	0.83[CEU][hapmap]
rs512497	0.86[EUR][1000 genomes]
rs513031	0.83[CEU][hapmap]
rs514138	0.83[CEU][hapmap]
rs520470	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs520599	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs527399	0.84[EUR][1000 genomes]
rs529464	0.85[EUR][1000 genomes]
rs530156	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs530458	0.86[EUR][1000 genomes]
rs532017	0.86[EUR][1000 genomes]
rs532756	0.84[EUR][1000 genomes]
rs532785	0.86[EUR][1000 genomes]
rs537190	0.86[EUR][1000 genomes]
rs538016	0.86[EUR][1000 genomes]
rs539026	0.86[EUR][1000 genomes]
rs539427	0.83[CEU][hapmap]
rs539754	0.80[CEU][hapmap]
rs540164	0.86[EUR][1000 genomes]
rs543305	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs543805	0.84[EUR][1000 genomes]
rs544263	0.83[CEU][hapmap]
rs544542	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs545472	0.86[EUR][1000 genomes]
rs547757	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs548644	0.86[EUR][1000 genomes]
rs549464	0.86[EUR][1000 genomes]
rs551459	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs551476	0.81[EUR][1000 genomes]
rs553437	0.86[EUR][1000 genomes]
rs555134	0.84[EUR][1000 genomes]
rs556711	0.86[EUR][1000 genomes]
rs556807	0.86[EUR][1000 genomes]
rs559277	0.81[EUR][1000 genomes]
rs562369	0.86[EUR][1000 genomes]
rs563271	0.84[EUR][1000 genomes]
rs563358	0.82[EUR][1000 genomes]
rs564042	0.86[EUR][1000 genomes]
rs568143	0.83[CEU][hapmap]
rs568369	0.86[EUR][1000 genomes]
rs568563	0.86[EUR][1000 genomes]
rs569142	0.86[EUR][1000 genomes]
rs574909	0.81[EUR][1000 genomes]
rs575461	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs577530	0.86[EUR][1000 genomes]
rs579712	0.84[EUR][1000 genomes]
rs580792	0.81[EUR][1000 genomes]
rs6458682	0.82[EUR][1000 genomes]
rs6902604	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6902615	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6903158	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6922862	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6923065	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6927463	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6935826	0.83[EUR][1000 genomes]
rs72869253	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870365	0.86[EUR][1000 genomes]
rs7450140	0.84[EUR][1000 genomes]
rs7764755	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9349492	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9357609	0.82[EUR][1000 genomes]
rs9357610	0.86[EUR][1000 genomes]
rs9357612	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9367355	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369883	0.81[EUR][1000 genomes]
rs9369884	0.84[EUR][1000 genomes]
rs9369886	0.86[EUR][1000 genomes]
rs9369902	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9381766	0.84[EUR][1000 genomes]
rs9381767	0.86[EUR][1000 genomes]
rs9381770	0.83[CEU][hapmap]
rs9395477	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv915806	chr6:49313295-49430422	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11757098	MUT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49383400-49399800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:49389600-49401200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:49391000-49401200	Weak transcription	Left Ventricle	heart
4	chr6:49392400-49403800	Weak transcription	Right Ventricle	heart
5	chr6:49392800-49400400	Weak transcription	Ovary	ovary
6	chr6:49393400-49406400	Weak transcription	Lung	lung
7	chr6:49393600-49399400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:49394000-49400400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:49394600-49399200	Weak transcription	Brain Germinal Matrix	brain
10	chr6:49394600-49399600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:49394600-49400200	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:49394800-49403200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:49395000-49402000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:49395200-49399200	Weak transcription	Fetal Lung	lung
15	chr6:49395200-49400400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:49395200-49400400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:49395200-49406400	Weak transcription	Fetal Intestine Small	intestine
18	chr6:49395200-49406400	Weak transcription	Fetal Stomach	stomach
19	chr6:49395200-49406400	Weak transcription	Gastric	stomach
20	chr6:49395200-49406400	Weak transcription	Spleen	Spleen
21	chr6:49395400-49400800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:49395400-49400800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr6:49395400-49400800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:49395400-49402400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:49395400-49406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:49395400-49429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:49395600-49400800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:49395600-49403200	Weak transcription	Psoas Muscle	Psoas
29	chr6:49395600-49406400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:49395600-49406400	Weak transcription	Thymus	Thymus
31	chr6:49395800-49399000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:49395800-49400400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr6:49395800-49400400	Weak transcription	Fetal Kidney	kidney
34	chr6:49395800-49402400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:49395800-49406600	Weak transcription	Colonic Mucosa	Colon
36	chr6:49396000-49401000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:49396000-49401000	Weak transcription	Brain Anterior Caudate	brain
38	chr6:49396000-49402400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:49396000-49420800	Strong transcription	Liver	Liver
40	chr6:49396000-49427400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:49396200-49420400	Strong transcription	Adipose Nuclei	Adipose
42	chr6:49396400-49403400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:49396400-49407600	Weak transcription	HSMMtube	muscle
44	chr6:49396400-49429400	Weak transcription	Stomach Mucosa	stomach
45	chr6:49396600-49399800	Weak transcription	Brain Angular Gyrus	brain
46	chr6:49396600-49400200	Weak transcription	Dnd41	blood
47	chr6:49396600-49402000	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:49396600-49402400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:49396600-49408800	Strong transcription	Primary T cells from cord blood	blood
50	chr6:49396600-49411000	Weak transcription	Fetal Heart	heart

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