Variant report

Variant	rs10159002
Chromosome Location	chr1:246938049-246938050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCCPDH-1	chr1:246935603-246939074	ENSG00000260855.1
2	lnc-SCCPDH-1	chr1:246937472-246939075	NONHSAT010724

Extended variants
information (count: 79 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10127783	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754532	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10754533	0.88[CHB][hapmap]
rs10802442	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802443	0.84[ASN][1000 genomes]
rs10924820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10924823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027222	0.85[ASN][1000 genomes]
rs12049149	0.83[EUR][1000 genomes]
rs12058428	0.84[EUR][1000 genomes]
rs12085330	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090470	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12117291	0.82[ASN][1000 genomes]
rs12120124	0.80[ASN][1000 genomes]
rs12122102	1.00[CHB][hapmap]
rs12132038	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12135184	0.82[CEU][hapmap]
rs12142760	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12144408	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3007316	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3007317	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3007318	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3007322	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3007323	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3007324	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3007411	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34649985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34989088	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3795462	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs3795463	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795464	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4130316	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4130317	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244628	0.86[EUR][1000 genomes]
rs4244630	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4926441	0.86[EUR][1000 genomes]
rs4926451	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs4926453	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs4926454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926455	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4926457	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926459	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6426323	0.87[CHB][hapmap]
rs6426326	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6426332	0.86[EUR][1000 genomes]
rs6426334	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs6664883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685364	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686584	0.86[EUR][1000 genomes]
rs72764626	0.90[ASN][1000 genomes]
rs7364715	0.93[ASN][1000 genomes]
rs7365076	0.84[ASN][1000 genomes]
rs7366377	0.85[ASN][1000 genomes]
rs7416239	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7513803	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs7532928	0.87[CHB][hapmap]
rs7537149	0.84[EUR][1000 genomes]
rs7549965	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs7556120	0.86[EUR][1000 genomes]
rs9426218	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9426269	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9426271	0.82[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS 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	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv3415065	chr1:246937990-246938230	Strong transcription Weak transcription	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
5	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
8	chr1:246920800-246944200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:246921200-246943200	Strong transcription	Dnd41	blood
10	chr1:246921600-246945800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:246922200-246944600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:246923200-246945000	Strong transcription	Fetal Muscle Leg	muscle
13	chr1:246924000-246941200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr1:246924000-246944200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:246924400-246939200	Weak transcription	Colonic Mucosa	Colon
16	chr1:246924400-246945800	Weak transcription	Primary B cells from cord blood	blood
17	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:246926400-246939200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:246928800-246944800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:246930600-246939000	Weak transcription	Thymus	Thymus
21	chr1:246931200-246940600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:246932000-246939200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:246932400-246939000	Weak transcription	Pancreas	Pancrea
24	chr1:246932400-246945800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:246932400-246952000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:246932600-246938600	Weak transcription	Brain Substantia Nigra	brain
27	chr1:246932600-246939200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:246932600-246939400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:246932600-246948000	Strong transcription	Liver	Liver
30	chr1:246932600-246948600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:246932600-246948600	Weak transcription	Esophagus	oesophagus
32	chr1:246932800-246938400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:246932800-246938600	Weak transcription	HUVEC	blood vessel
34	chr1:246932800-246938600	Weak transcription	Osteobl	bone
35	chr1:246932800-246939000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:246932800-246939200	Weak transcription	Brain Angular Gyrus	brain
37	chr1:246932800-246939200	Weak transcription	Gastric	stomach
38	chr1:246932800-246939200	Weak transcription	Spleen	Spleen
39	chr1:246932800-246939400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:246932800-246939400	Weak transcription	NHLF	lung
41	chr1:246932800-246945000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:246932800-246945600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:246932800-246945800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:246932800-246948800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:246932800-246952400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:246932800-246956400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:246933000-246938400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:246933000-246938400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:246933000-246938600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:246933000-246939200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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