Variant report

Variant	rs11615961
Chromosome Location	chr12:31536772-31536773
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM60A-3	chr12:31535160-31537109	NONHSAT027548

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1012154	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs10743757	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10743758	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs10743759	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10771827	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771828	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10771838	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10771843	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10771844	0.84[EUR][1000 genomes]
rs10771845	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10771846	0.84[EUR][1000 genomes]
rs10843942	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10843947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10843958	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843959	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843963	0.85[EUR][1000 genomes]
rs11051418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051435	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11051437	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11051439	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11051441	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1150942	0.86[CHB][hapmap]
rs1150953	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1150954	0.86[CHB][hapmap]
rs1150955	0.86[CHB][hapmap]
rs1259235	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1259236	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1259386	0.83[CHB][hapmap]
rs1259409	0.86[CHB][hapmap]
rs1259428	0.92[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1259432	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs1259437	0.86[CHB][hapmap]
rs1272773	0.86[CHB][hapmap]
rs1469673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1677189	0.86[CHB][hapmap]
rs1716216	0.93[CHB][hapmap]
rs1996693	0.85[EUR][1000 genomes]
rs2116704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2352048	0.81[EUR][1000 genomes]
rs2568884	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs2617190	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2617191	0.86[CHB][hapmap]
rs2617200	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs2682697	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2682700	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2888762	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35906870	0.80[AMR][1000 genomes]
rs3803113	0.81[EUR][1000 genomes]
rs3844573	0.89[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3850965	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4482118	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4930980	0.85[EUR][1000 genomes]
rs4931488	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4931501	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4931506	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4931507	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6416254	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6487989	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6487992	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66521153	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708200	0.81[AMR][1000 genomes]
rs708209	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs708214	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs708219	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7133082	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7134365	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135856	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7136476	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7136943	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7137406	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71440988	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7294574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303447	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7303848	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7307593	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7307616	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7313118	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7313158	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7313689	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7314417	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs793146	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs793154	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793157	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs793174	0.86[CHB][hapmap]
rs793176	0.93[CHB][hapmap]
rs793177	0.86[CHB][hapmap]
rs793180	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs793184	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs793186	0.86[CHB][hapmap]
rs7954023	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7954595	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7959877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7962896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7963161	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7967832	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7968291	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7974437	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7975761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7977453	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs899159	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs9738834	0.85[EUR][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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31523400-31537600	Weak transcription	Fetal Brain Female	brain
2	chr12:31523800-31538200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:31524400-31538200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:31524400-31540200	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:31524800-31537200	Weak transcription	Fetal Intestine Large	intestine
6	chr12:31524800-31538000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:31530800-31538000	Weak transcription	Liver	Liver
8	chr12:31530800-31541400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:31531800-31539600	Weak transcription	HSMM	muscle
10	chr12:31532800-31538800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:31533600-31537400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:31534000-31539000	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:31534200-31538000	Weak transcription	A549	lung
14	chr12:31534400-31540400	Weak transcription	Psoas Muscle	Psoas
15	chr12:31534600-31537200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:31534800-31538400	Weak transcription	Ovary	ovary
17	chr12:31534800-31538600	Weak transcription	Fetal Intestine Small	intestine
18	chr12:31534800-31541800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:31535000-31538000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:31535000-31538200	Weak transcription	Adipose Nuclei	Adipose
21	chr12:31535000-31538200	Weak transcription	Left Ventricle	heart
22	chr12:31535000-31539000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:31535200-31538000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:31535200-31538200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:31535200-31538200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr12:31535200-31538200	Weak transcription	Brain Anterior Caudate	brain
27	chr12:31535400-31538000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr12:31535400-31538200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr12:31535400-31538200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:31535400-31538200	Weak transcription	Aorta	Aorta
31	chr12:31535400-31538400	Weak transcription	Brain Germinal Matrix	brain
32	chr12:31535400-31538800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:31535400-31541800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr12:31535600-31537200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr12:31535600-31539000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr12:31535600-31560600	Weak transcription	Osteobl	bone
37	chr12:31535800-31538200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:31535800-31539400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:31535800-31544000	Weak transcription	Fetal Lung	lung
40	chr12:31536000-31538000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr12:31536000-31539000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:31536000-31540400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:31536000-31550600	Weak transcription	Right Ventricle	heart
44	chr12:31536200-31537200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr12:31536200-31538000	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr12:31536200-31538200	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr12:31536200-31538400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr12:31536400-31538400	Weak transcription	Brain Angular Gyrus	brain
49	chr12:31536400-31538600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:31536400-31539000	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links