Variant report

Variant	rs2391140
Chromosome Location	chr1:92761654-92761655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10747411	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782838	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875348	1.00[YRI][hapmap]
rs11166568	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11166575	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226177	1.00[ASN][1000 genomes]
rs1226188	1.00[ASN][1000 genomes]
rs1234874	1.00[ASN][1000 genomes]
rs1386585	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487537	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487539	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131767	1.00[ASN][1000 genomes]
rs1748178	1.00[ASN][1000 genomes]
rs17519833	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17579779	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1825813	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906279	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025607	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046621	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391139	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2763040	1.00[ASN][1000 genomes]
rs3103177	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103180	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122320	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131815	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131824	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131831	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4247165	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475034	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs476490	1.00[ASN][1000 genomes]
rs481384	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs481677	1.00[ASN][1000 genomes]
rs487443	1.00[ASN][1000 genomes]
rs495446	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs501872	1.00[ASN][1000 genomes]
rs510857	1.00[ASN][1000 genomes]
rs517404	1.00[ASN][1000 genomes]
rs523692	1.00[ASN][1000 genomes]
rs524989	1.00[ASN][1000 genomes]
rs525834	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs530815	1.00[ASN][1000 genomes]
rs532031	1.00[ASN][1000 genomes]
rs533124	1.00[ASN][1000 genomes]
rs533418	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs537754	1.00[ASN][1000 genomes]
rs538054	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs541168	1.00[ASN][1000 genomes]
rs544556	1.00[ASN][1000 genomes]
rs548100	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs548141	1.00[ASN][1000 genomes]
rs552468	1.00[ASN][1000 genomes]
rs553173	1.00[ASN][1000 genomes]
rs562119	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs564077	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs566576	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs579668	1.00[ASN][1000 genomes]
rs59679370	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6603963	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603967	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604089	0.93[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604091	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668685	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692060	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512301	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518357	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7520275	1.00[CHB][hapmap]
rs7542747	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545445	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547429	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs912795	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv871352	chr1:92761127-92807238	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2391140	RPL10A	trans	cerebellum	SCAN
rs2391140	FAM69A	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92707200-92764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:92709000-92762800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:92710600-92762000	Weak transcription	Fetal Brain Male	brain
4	chr1:92710600-92763400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:92710600-92764000	Weak transcription	Gastric	stomach
6	chr1:92711000-92763600	Weak transcription	HSMMtube	muscle
7	chr1:92711200-92764000	Weak transcription	Spleen	Spleen
8	chr1:92719400-92764000	Weak transcription	Pancreas	Pancrea
9	chr1:92720000-92763800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:92722400-92763400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:92723000-92763800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:92724600-92763800	Weak transcription	Brain Substantia Nigra	brain
13	chr1:92725800-92764000	Weak transcription	Colonic Mucosa	Colon
14	chr1:92727000-92763800	Weak transcription	Right Ventricle	heart
15	chr1:92727200-92763800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:92729800-92763800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:92732000-92763600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:92736000-92763600	Weak transcription	Liver	Liver
19	chr1:92736800-92763800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:92738000-92763800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:92738400-92763800	Weak transcription	Brain Anterior Caudate	brain
22	chr1:92738800-92763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:92743200-92763600	Weak transcription	NHDF-Ad	bronchial
24	chr1:92744000-92764000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:92745600-92764000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:92745800-92763800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:92745800-92763800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:92745800-92764000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:92745800-92764000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:92746000-92761800	Weak transcription	Esophagus	oesophagus
31	chr1:92746000-92763600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:92746000-92763800	Weak transcription	Aorta	Aorta
33	chr1:92746000-92763800	Weak transcription	Fetal Intestine Small	intestine
34	chr1:92746000-92764000	Weak transcription	Lung	lung
35	chr1:92746400-92762400	Weak transcription	Fetal Brain Female	brain
36	chr1:92751600-92763400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:92751600-92763800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:92752400-92763600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:92752800-92763800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:92753200-92763400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:92754200-92761800	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:92755000-92763200	Weak transcription	Brain Germinal Matrix	brain
43	chr1:92755000-92763600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:92755400-92761800	Weak transcription	HUVEC	blood vessel
45	chr1:92755400-92763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:92755400-92763400	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:92755400-92763600	Weak transcription	Adipose Nuclei	Adipose
48	chr1:92755400-92763600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:92755400-92763800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:92755400-92764000	Weak transcription	Left Ventricle	heart

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