Variant report

Variant	rs10099137
Chromosome Location	chr8:10662237-10662238
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	chr8:10661041..10663071-chr8:10663223..10664921,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP1L1-7	chr8:10660588-10662320	NONHSAT125018

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10089615	0.82[CHB][hapmap]
rs10091836	0.89[ASN][1000 genomes]
rs10091961	0.86[ASN][1000 genomes]
rs10092781	0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10094907	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10095737	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10097283	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs10097531	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10099021	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10099907	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10099928	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10105487	0.83[CHB][hapmap]
rs10107180	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10107303	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10109034	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10109550	0.85[CEU][hapmap]
rs10113332	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10113343	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1115866	0.81[CHB][hapmap]
rs11250069	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11250070	0.88[ASN][1000 genomes]
rs11250071	0.86[ASN][1000 genomes]
rs11250073	0.83[CHB][hapmap]
rs11250074	0.81[CHB][hapmap]
rs11250077	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs11250079	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12056936	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12542888	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs12544044	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12550169	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12550720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12679010	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs12679155	0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12679178	0.87[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs12680846	0.83[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12681175	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12681375	0.87[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12682565	0.81[CHB][hapmap]
rs1430867	0.84[ASN][1000 genomes]
rs1469557	0.86[YRI][hapmap]
rs1544981	0.80[CEU][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs1549794	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17152302	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17152305	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17152520	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1821001	0.88[ASN][1000 genomes]
rs2005309	0.82[ASN][1000 genomes]
rs2005311	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2033369	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2052963	0.95[CEU][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs2116092	0.84[ASN][1000 genomes]
rs2116095	0.81[CHB][hapmap]
rs2116096	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271356	0.89[CEU][hapmap]
rs2280047	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2409651	0.89[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs2409663	0.82[CHB][hapmap]
rs2409669	0.81[CHB][hapmap]
rs28429578	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28592638	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4321967	0.82[CHB][hapmap]
rs4504595	0.83[ASN][1000 genomes]
rs4593498	0.83[ASN][1000 genomes]
rs60011038	0.81[EUR][1000 genomes]
rs6601520	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601524	0.89[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6601525	0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6981530	0.85[ASN][1000 genomes]
rs6985218	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6989072	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6989846	0.84[CEU][hapmap]
rs6992039	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6994595	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6995541	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7002137	0.86[ASN][1000 genomes]
rs7005531	0.85[CEU][hapmap]
rs7010709	0.86[YRI][hapmap]
rs7010926	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7014168	0.95[CEU][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7014285	0.86[ASN][1000 genomes]
rs7015129	0.87[ASN][1000 genomes]
rs714371	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs733395	0.85[ASN][1000 genomes]
rs733396	0.85[ASN][1000 genomes]
rs73542560	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73544343	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs736668	0.85[ASN][1000 genomes]
rs736669	0.85[ASN][1000 genomes]
rs752446	0.81[ASN][1000 genomes]
rs7820819	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7823088	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7823521	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7824384	0.85[CEU][hapmap]
rs7826180	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7826189	0.95[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7826218	0.86[ASN][1000 genomes]
rs7826392	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7826458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7830528	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7834466	0.80[CHB][hapmap]
rs7836194	0.84[JPT][hapmap]
rs7838341	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891554	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs891555	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs891556	0.82[ASN][1000 genomes]
rs919555	0.86[ASN][1000 genomes]
rs9644730	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9657541	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active 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	37 gene(s)	inside rSNPs	diseases
2	nsv1026802	chr8:10576444-10754489	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv539469	chr8:10576444-10754489	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1017836	chr8:10591801-10803617	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1034988	chr8:10591801-10804243	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519768	chr8:10600254-10691993	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1024806	chr8:10605438-10662555	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv831232	chr8:10606053-10774948	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
9	nsv519376	chr8:10611708-10691993	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv429860	chr8:10615990-10685890	Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1019754	chr8:10617908-10700140	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
12	nsv539471	chr8:10617908-10700140	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv1031726	chr8:10627742-10749369	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10618800-10665200	Weak transcription	Fetal Brain Female	brain
2	chr8:10620000-10669800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr8:10623400-10662600	Weak transcription	Fetal Thymus	thymus
4	chr8:10623400-10662800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr8:10623400-10665000	Weak transcription	Fetal Intestine Large	intestine
6	chr8:10623600-10667000	Weak transcription	Thymus	Thymus
7	chr8:10635400-10664400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr8:10640200-10669800	Weak transcription	Aorta	Aorta
9	chr8:10640600-10662800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr8:10641200-10665000	Weak transcription	Dnd41	blood
11	chr8:10645000-10670000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr8:10646800-10662800	Weak transcription	GM12878-XiMat	blood
13	chr8:10647000-10674400	Weak transcription	Right Ventricle	heart
14	chr8:10647000-10681200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr8:10647200-10673600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr8:10647800-10669800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr8:10648200-10663600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr8:10648200-10669800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr8:10648200-10683400	Weak transcription	Brain Angular Gyrus	brain
20	chr8:10650000-10676200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr8:10650600-10662600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr8:10650600-10664000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr8:10650600-10664200	Weak transcription	Spleen	Spleen
24	chr8:10650600-10665000	Weak transcription	Fetal Intestine Small	intestine
25	chr8:10650600-10665000	Weak transcription	Fetal Muscle Leg	muscle
26	chr8:10650600-10669000	Weak transcription	Fetal Stomach	stomach
27	chr8:10650600-10671200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr8:10650800-10669400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr8:10653600-10664400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr8:10654400-10662600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr8:10655800-10664400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr8:10657200-10662600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr8:10657200-10670000	Weak transcription	Lung	lung
34	chr8:10657400-10681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr8:10657400-10685800	Weak transcription	Psoas Muscle	Psoas
36	chr8:10657600-10665000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr8:10657600-10670000	Weak transcription	Gastric	stomach
38	chr8:10657600-10674200	Weak transcription	Pancreas	Pancrea
39	chr8:10657600-10674600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr8:10657600-10674600	Weak transcription	Esophagus	oesophagus
41	chr8:10657600-10674600	Weak transcription	Left Ventricle	heart
42	chr8:10657600-10681800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr8:10657800-10662400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr8:10657800-10665000	Weak transcription	Adipose Nuclei	Adipose
45	chr8:10657800-10673000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr8:10657800-10673200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr8:10657800-10674400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr8:10657800-10674600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr8:10657800-10680600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr8:10657800-10680600	Weak transcription	HSMMtube	muscle

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