Variant report

Variant	rs4951638
Chromosome Location	chr1:212931215-212931216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10494955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054733	0.81[ASN][1000 genomes]
rs10863990	0.96[ASN][1000 genomes]
rs10863993	0.98[ASN][1000 genomes]
rs10863995	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863998	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863999	0.95[ASN][1000 genomes]
rs10864000	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10864001	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11120011	0.98[ASN][1000 genomes]
rs11120012	0.99[ASN][1000 genomes]
rs11120013	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120019	0.94[ASN][1000 genomes]
rs11120024	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11120025	0.85[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs11120026	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120032	0.83[ASN][1000 genomes]
rs11120037	0.82[ASN][1000 genomes]
rs11120039	0.80[ASN][1000 genomes]
rs1133462	0.86[ASN][1000 genomes]
rs12064985	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12088916	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12095846	0.82[ASN][1000 genomes]
rs12097897	0.84[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12125321	0.93[ASN][1000 genomes]
rs12126017	0.95[ASN][1000 genomes]
rs12130945	0.86[ASN][1000 genomes]
rs12132316	0.99[ASN][1000 genomes]
rs12136046	0.98[ASN][1000 genomes]
rs12136834	0.98[ASN][1000 genomes]
rs12722742	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12734543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12737398	0.86[ASN][1000 genomes]
rs12741704	0.92[ASN][1000 genomes]
rs12743402	0.90[ASN][1000 genomes]
rs12744602	0.82[ASN][1000 genomes]
rs12747251	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12758602	0.81[ASN][1000 genomes]
rs12759287	0.87[ASN][1000 genomes]
rs2359322	0.86[ASN][1000 genomes]
rs34274815	0.85[ASN][1000 genomes]
rs3820679	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3862953	0.86[ASN][1000 genomes]
rs4951457	0.85[CEU][hapmap]
rs4951460	0.83[EUR][1000 genomes]
rs4951463	0.92[ASN][1000 genomes]
rs61829243	0.81[ASN][1000 genomes]
rs6540761	0.91[ASN][1000 genomes]
rs6540763	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6661720	0.98[ASN][1000 genomes]
rs6669492	0.92[ASN][1000 genomes]
rs6679350	0.92[ASN][1000 genomes]
rs6679549	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6689604	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6690689	0.98[ASN][1000 genomes]
rs6693311	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6694452	0.93[ASN][1000 genomes]
rs6697507	0.81[ASN][1000 genomes]
rs6700410	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs6702025	0.93[ASN][1000 genomes]
rs6702611	0.95[ASN][1000 genomes]
rs7554105	0.86[ASN][1000 genomes]
rs7556272	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv1005983	chr1:212917531-212947521	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs4951638	C4BPA	cis	cerebellum	SCAN
rs4951638	LQK1	cis	parietal	SCAN
rs4951638	LQK1	cis	lesional skin	skin_eQTL
rs4951638	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs4951638	NSL1	cis	lymphoblastoid	seeQTL
rs4951638	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs4951638	C1orf227	cis	parietal	SCAN
rs4951638	BPIL3	trans	cerebellum	SCAN
rs4951638	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs4951638	C1orf227	cis	cerebellum	SCAN
rs4951638	LQK1	cis	uninvolved skin	skin_eQTL
rs4951638	NCRNA00292	cis	lymphoblastoid	seeQTL
rs4951638	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs4951638	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs4951638	VASH2	cis	parietal	SCAN
rs4951638	LQK1	cis	cerebellum	SCAN
rs4951638	LOC642946	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
2	chr1:212895600-212964600	Weak transcription	Gastric	stomach
3	chr1:212898800-212934000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:212900400-212932600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:212900400-212936200	Weak transcription	Aorta	Aorta
6	chr1:212901400-212954000	Weak transcription	NH-A	brain
7	chr1:212902200-212941800	Weak transcription	Fetal Kidney	kidney
8	chr1:212902600-212943600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:212908000-212933200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:212912000-212935800	Weak transcription	K562	blood
11	chr1:212915400-212932600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:212915400-212933400	Weak transcription	Ovary	ovary
13	chr1:212915400-212934400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:212915400-212936000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:212915400-212942000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:212922200-212939600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:212923600-212932800	Weak transcription	Fetal Intestine Large	intestine
18	chr1:212923600-212935400	Weak transcription	Lung	lung
19	chr1:212923600-212956200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
21	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:212923800-212932600	Weak transcription	Spleen	Spleen
23	chr1:212923800-212935800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:212923800-212935800	Weak transcription	Placenta	Placenta
25	chr1:212923800-212947200	Weak transcription	A549	lung
26	chr1:212923800-212957600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:212923800-212964200	Weak transcription	HMEC	breast
28	chr1:212924000-212954200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:212926600-212933800	Weak transcription	HSMM	muscle
30	chr1:212926600-212939600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:212926600-212941800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:212926600-212954200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:212926800-212932800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:212926800-212934000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:212926800-212936000	Weak transcription	Esophagus	oesophagus
37	chr1:212926800-212939600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:212926800-212940600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:212926800-212940800	Weak transcription	NHLF	lung
40	chr1:212926800-212942200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:212926800-212942400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:212926800-212942800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:212926800-212942800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:212926800-212947800	Weak transcription	NHDF-Ad	bronchial
45	chr1:212926800-212948000	Weak transcription	Osteobl	bone
46	chr1:212926800-212954200	Weak transcription	Hela-S3	cervix
47	chr1:212927000-212941800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:212927400-212942400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
50	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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