Variant report

Variant	rs3811405
Chromosome Location	chr1:151227371-151227372
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1056847	0.86[JPT][hapmap]
rs10749660	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs10788801	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap];0.92[ASN][1000 genomes]
rs10788803	0.86[JPT][hapmap]
rs10888408	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs10888409	0.86[JPT][hapmap]
rs10888410	0.86[JPT][hapmap]
rs11204785	0.83[GIH][hapmap];0.90[JPT][hapmap]
rs11204791	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs11589120	0.91[ASN][1000 genomes]
rs1536617	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs16827941	0.90[JPT][hapmap]
rs1752387	0.90[JPT][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap]
rs1892196	0.85[GIH][hapmap]
rs2025900	0.95[JPT][hapmap];0.82[MEX][hapmap]
rs2031797	0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs2275900	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs2769267	0.85[JPT][hapmap];0.83[MEX][hapmap]
rs2769268	0.95[JPT][hapmap]
rs2769273	0.95[JPT][hapmap];0.83[MEX][hapmap]
rs2800946	0.95[JPT][hapmap];0.83[MEX][hapmap]
rs2800953	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs3811406	0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.82[ASN][1000 genomes]
rs4246525	0.81[JPT][hapmap]
rs4520422	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs4636463	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4970944	0.85[GIH][hapmap];0.90[JPT][hapmap]
rs4970948	0.86[JPT][hapmap]
rs4971013	0.88[GIH][hapmap];0.90[JPT][hapmap]
rs4971017	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4971018	1.00[ASW][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4971023	0.90[JPT][hapmap]
rs4971027	0.86[JPT][hapmap]
rs4971028	0.86[ASN][1000 genomes]
rs4971029	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4971030	0.86[JPT][hapmap]
rs6587559	0.88[GIH][hapmap];0.90[JPT][hapmap]
rs6587562	0.86[JPT][hapmap]
rs6678528	1.00[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs6686402	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs6695344	0.84[GIH][hapmap];0.85[JPT][hapmap]
rs6695901	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6702612	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7527032	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs7532935	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs7539584	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs7544947	0.88[GIH][hapmap];0.90[JPT][hapmap]
rs7545024	0.95[ASN][1000 genomes]
rs7545392	0.81[JPT][hapmap]
rs7552226	0.86[ASW][hapmap];0.88[YRI][hapmap]
rs943637	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3811405	HORMAD1	cis	parietal	SCAN
rs3811405	PSMD4	cis	parietal	SCAN
rs3811405	CTSS	cis	cerebellum	SCAN
rs3811405	FLG	cis	cerebellum	SCAN
rs3811405	RFX5	cis	cerebellum	SCAN
rs3811405	PSMD4	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151226400-151227400	Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr1:151226400-151227800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:151226600-151227400	Active TSS	Primary T cells from cord blood	blood
4	chr1:151226600-151227400	Active TSS	Primary hematopoietic stem cells	blood
5	chr1:151226600-151227600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:151226600-151227600	Active TSS	Rectal Smooth Muscle	rectum
7	chr1:151226600-151227800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:151226600-151227800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:151226600-151227800	Active TSS	Primary B cells from peripheral blood	blood
10	chr1:151226600-151227800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:151226600-151227800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:151226600-151227800	Active TSS	Brain Anterior Caudate	brain
13	chr1:151226600-151227800	Active TSS	Brain Hippocampus Middle	brain
14	chr1:151226600-151227800	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:151226600-151227800	Active TSS	Brain Substantia Nigra	brain
16	chr1:151226600-151227800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr1:151226600-151227800	Active TSS	Fetal Brain Female	brain
18	chr1:151226600-151227800	Active TSS	Fetal Muscle Leg	muscle
19	chr1:151226600-151227800	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr1:151226600-151227800	Active TSS	Stomach Smooth Muscle	stomach
21	chr1:151226600-151228000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:151226600-151228000	Active TSS	Colonic Mucosa	Colon
23	chr1:151226600-151228000	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr1:151226600-151228000	Active TSS	Fetal Intestine Large	intestine
25	chr1:151226600-151228000	Active TSS	Fetal Muscle Trunk	muscle
26	chr1:151226600-151228200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:151226600-151228200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr1:151226600-151228200	Active TSS	Right Atrium	heart
29	chr1:151226600-151228200	Active TSS	Right Ventricle	heart
30	chr1:151226600-151228400	Active TSS	Psoas Muscle	Psoas
31	chr1:151226600-151228600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:151226600-151228600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:151226800-151227400	Active TSS	HepG2	liver
34	chr1:151226800-151227600	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr1:151226800-151227600	Active TSS	Adipose Nuclei	Adipose
36	chr1:151226800-151227600	Active TSS	Fetal Kidney	kidney
37	chr1:151226800-151227600	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr1:151226800-151227600	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr1:151226800-151227600	Active TSS	Spleen	Spleen
40	chr1:151226800-151227800	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr1:151226800-151227800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:151226800-151227800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:151226800-151227800	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr1:151226800-151227800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr1:151226800-151227800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:151226800-151227800	Active TSS	Liver	Liver
47	chr1:151226800-151227800	Active TSS	Brain Cingulate Gyrus	brain
48	chr1:151226800-151227800	Active TSS	Colon Smooth Muscle	Colon
49	chr1:151226800-151227800	Active TSS	Duodenum Mucosa	Duodenum
50	chr1:151226800-151227800	Active TSS	Fetal Lung	lung

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