Variant report

Variant	rs951623
Chromosome Location	chr1:212399062-212399063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1009622	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs10863953	0.87[EUR][1000 genomes]
rs10863954	0.87[EUR][1000 genomes]
rs11119879	0.87[EUR][1000 genomes]
rs11119880	0.82[EUR][1000 genomes]
rs11119883	0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs11119884	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119885	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119887	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12028026	0.90[EUR][1000 genomes]
rs12038888	0.82[EUR][1000 genomes]
rs12073206	0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12402397	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389369	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389370	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1389371	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs1472226	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967114	0.88[EUR][1000 genomes]
rs1967116	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1967117	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001234	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012917	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2087946	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307128	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2884512	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351377	0.80[ASN][1000 genomes]
rs351378	0.80[ASN][1000 genomes]
rs351379	0.80[ASN][1000 genomes]
rs351386	0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs351408	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs35209719	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816912	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4362041	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4500383	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4558048	0.87[EUR][1000 genomes]
rs4951581	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951582	0.86[ASN][1000 genomes]
rs6540729	0.88[EUR][1000 genomes]
rs6540731	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540732	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6540733	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6540734	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540735	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657900	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6668866	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6679796	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6695681	0.89[EUR][1000 genomes]
rs7511781	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7515645	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518329	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7519168	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530375	0.87[EUR][1000 genomes]
rs7537062	0.89[EUR][1000 genomes]
rs7542973	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544225	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs7552021	0.88[EUR][1000 genomes]
rs867584	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903120	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs903121	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs951623	NSL1	cis	cerebellum	SCAN
rs951623	TMEM206	cis	cerebellum	SCAN
rs951623	FCAMR	cis	parietal	SCAN
rs951623	LGTN	cis	cerebellum	SCAN
rs951623	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs951623	TMEM206	cis	Esophagus Mucosa	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212392000-212399400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:212392200-212399200	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:212392600-212399200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:212392600-212404800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:212393600-212399200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:212393600-212399200	Weak transcription	Small Intestine	intestine
7	chr1:212394800-212399200	Weak transcription	Gastric	stomach
8	chr1:212395200-212399200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:212395400-212399200	Weak transcription	Left Ventricle	heart
10	chr1:212395600-212399200	Weak transcription	Right Atrium	heart
11	chr1:212397400-212400000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:212397400-212400200	Enhancers	Adipose Nuclei	Adipose
13	chr1:212397600-212400000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:212397800-212400000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:212397800-212400200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:212397800-212400200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:212398000-212402000	Enhancers	HepG2	liver
18	chr1:212398200-212400000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:212398200-212400000	Enhancers	Fetal Thymus	thymus
20	chr1:212398400-212399200	Weak transcription	Lung	lung
21	chr1:212398400-212399400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:212398400-212399800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr1:212398400-212400000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr1:212398400-212400000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr1:212398400-212400000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:212398400-212400200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr1:212398600-212399200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:212398600-212399200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:212398600-212399600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:212398600-212399600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:212398600-212399800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:212398600-212399800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr1:212398600-212399800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr1:212398600-212399800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:212398600-212399800	Enhancers	Brain Anterior Caudate	brain
36	chr1:212398600-212399800	Enhancers	Brain Cingulate Gyrus	brain
37	chr1:212398600-212399800	Enhancers	Brain Substantia Nigra	brain
38	chr1:212398600-212399800	Enhancers	Fetal Kidney	kidney
39	chr1:212398600-212399800	Enhancers	Right Ventricle	heart
40	chr1:212398600-212400000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:212398600-212400000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr1:212398600-212402000	Enhancers	Liver	Liver
43	chr1:212398800-212399200	Enhancers	Brain Hippocampus Middle	brain
44	chr1:212398800-212399200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr1:212398800-212399400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr1:212398800-212399400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr1:212398800-212399400	Enhancers	Fetal Lung	lung
48	chr1:212398800-212399400	Enhancers	HUVEC	blood vessel
49	chr1:212398800-212399400	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr1:212398800-212399600	Enhancers	HUES6 Cell Line	embryonic stem cell

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