Variant report

Variant	rs4951649
Chromosome Location	chr1:213056493-213056494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10127459	1.00[ASN][1000 genomes]
rs10746436	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10779594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864003	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10864013	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10864017	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10864019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120033	1.00[ASN][1000 genomes]
rs11804466	1.00[CHB][hapmap]
rs11808834	1.00[CHB][hapmap]
rs11810592	1.00[CHB][hapmap]
rs12036735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408694	0.89[GIH][hapmap]
rs1284800	1.00[ASN][1000 genomes]
rs1284864	1.00[ASN][1000 genomes]
rs1390501	0.89[GIH][hapmap]
rs1615680	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1692178	1.00[ASN][1000 genomes]
rs1692179	1.00[ASN][1000 genomes]
rs1692180	1.00[ASN][1000 genomes]
rs17020044	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17020046	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1770777	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1770778	1.00[ASN][1000 genomes]
rs1874419	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047289	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047292	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2047293	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359321	1.00[CHB][hapmap]
rs2359324	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456815	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2644545	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2792558	1.00[ASN][1000 genomes]
rs2792560	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2792561	1.00[CHB][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs35976699	1.00[ASN][1000 genomes]
rs41315581	1.00[ASN][1000 genomes]
rs4418676	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4951468	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59252582	1.00[ASN][1000 genomes]
rs6540768	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666362	1.00[CEU][hapmap];1.00[CHB][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]
rs6667161	1.00[ASN][1000 genomes]
rs6674933	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688865	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6689134	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703612	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518378	1.00[CHB][hapmap]
rs7528119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533932	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542906	1.00[ASN][1000 genomes]
rs963327	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv998261	chr1:213029814-213064209	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv998979	chr1:213029814-213073013	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1007129	chr1:213037244-213083261	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4951649	NSL1	cis	parietal	SCAN
rs4951649	FLVCR1-AS1	cis	Artery Tibial	GTEx
rs4951649	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs4951649	LQK1	cis	parietal	SCAN
rs4951649	LOC642946	cis	multi-tissue	Pritchard
rs4951649	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs4951649	FLVCR1-AS1	cis	Whole Blood	GTEx
rs4951649	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx
rs4951649	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs4951649	FLVCR1	cis	lymphoblastoid	seeQTL
rs4951649	NCRNA00292	cis	lymphoblastoid	seeQTL
rs4951649	FLVCR1	cis	multi-tissue	Pritchard
rs4951649	FLVCR1-AS1	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213032600-213073000	Weak transcription	Colonic Mucosa	Colon
2	chr1:213032600-213073000	Weak transcription	Esophagus	oesophagus
3	chr1:213032800-213056800	Weak transcription	Fetal Thymus	thymus
4	chr1:213032800-213057800	Weak transcription	Placenta	Placenta
5	chr1:213032800-213061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:213032800-213062000	Weak transcription	Psoas Muscle	Psoas
7	chr1:213033600-213062000	Weak transcription	Thymus	Thymus
8	chr1:213034400-213058000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:213034400-213068000	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:213034600-213057000	Weak transcription	Brain Substantia Nigra	brain
11	chr1:213034600-213057000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:213034600-213057200	Weak transcription	Right Ventricle	heart
13	chr1:213034600-213061800	Weak transcription	Fetal Heart	heart
14	chr1:213034600-213067800	Weak transcription	NHLF	lung
15	chr1:213034600-213070600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:213035800-213073000	Weak transcription	Small Intestine	intestine
17	chr1:213036000-213070800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:213036200-213062000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:213036400-213062000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:213037600-213073200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:213038400-213072000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:213039600-213073000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:213040400-213073000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:213043200-213062000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:213043200-213073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:213044400-213063200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:213045000-213070800	Weak transcription	Pancreas	Pancrea
28	chr1:213046600-213066400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:213047000-213056800	Weak transcription	HSMM	muscle
30	chr1:213047000-213073600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:213047200-213059600	Weak transcription	Brain Angular Gyrus	brain
32	chr1:213047200-213061800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:213047200-213062000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:213047400-213059200	Weak transcription	HUVEC	blood vessel
35	chr1:213048800-213062600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:213049000-213056800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:213049000-213056800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:213049000-213058000	Weak transcription	Osteobl	bone
39	chr1:213049000-213059200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:213049000-213061800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr1:213049000-213073000	Weak transcription	HSMMtube	muscle
42	chr1:213049400-213063200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:213049600-213057000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:213049600-213057200	Weak transcription	Left Ventricle	heart
45	chr1:213049600-213058000	Weak transcription	A549	lung
46	chr1:213049600-213059600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:213049600-213062000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:213049800-213056600	Weak transcription	HMEC	breast
49	chr1:213049800-213057000	Weak transcription	Brain Anterior Caudate	brain
50	chr1:213049800-213057200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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