Variant report

Variant	rs1774249
Chromosome Location	chr1:212515613-212515614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212515457..212517203-chr1:212520374..212522955,2	K562	blood:
2	chr1:212514803..212516600-chr1:212518695..212521669,2	MCF-7	breast:
3	chr1:212507727..212512410-chr1:212514335..212517605,4	K562	blood:
4	chr1:212505148..212507116-chr1:212513885..212516139,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10019	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119904	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12023488	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024665	0.99[ASN][1000 genomes]
rs12033246	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035647	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12036130	0.80[EUR][1000 genomes]
rs12410664	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1389371	0.92[CEU][hapmap]
rs1992643	0.92[CEU][hapmap];0.93[CHB][hapmap]
rs2252044	0.89[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2298114	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3099112	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351380	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351386	0.96[CEU][hapmap];0.81[TSI][hapmap]
rs351393	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351398	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs351401	0.83[EUR][1000 genomes]
rs351408	0.96[CEU][hapmap]
rs3767861	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767862	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767863	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951588	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4951589	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659594	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7415843	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519959	0.89[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521853	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7544225	0.92[CEU][hapmap]
rs792445	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1774249	NENF	cis	Esophagus Mucosa	GTEx
rs1774249	TMEM206	cis	Esophagus Mucosa	GTEx
rs1774249	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212467400-212526000	Weak transcription	A549	lung
2	chr1:212479200-212525400	Weak transcription	Aorta	Aorta
3	chr1:212486200-212526000	Weak transcription	HUVEC	blood vessel
4	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
5	chr1:212493800-212533400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:212498000-212526200	Weak transcription	Fetal Brain Male	brain
7	chr1:212499800-212525400	Weak transcription	Gastric	stomach
8	chr1:212500000-212540400	Weak transcription	Stomach Mucosa	stomach
9	chr1:212501000-212533600	Weak transcription	Fetal Heart	heart
10	chr1:212501400-212525800	Weak transcription	Pancreas	Pancrea
11	chr1:212501400-212526200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:212501400-212540800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:212501800-212540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:212502200-212516600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:212502200-212526000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:212502400-212528200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:212502800-212541400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:212503000-212519200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:212504000-212548600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:212504200-212525600	Weak transcription	Spleen	Spleen
23	chr1:212504400-212537600	Weak transcription	Psoas Muscle	Psoas
24	chr1:212504800-212525800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:212504800-212526000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:212505000-212525600	Weak transcription	Colonic Mucosa	Colon
27	chr1:212505200-212531400	Weak transcription	HMEC	breast
28	chr1:212505800-212520200	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:212505800-212533200	Weak transcription	NH-A	brain
30	chr1:212506200-212518400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:212507400-212525400	Weak transcription	Esophagus	oesophagus
32	chr1:212507400-212525600	Weak transcription	Brain Anterior Caudate	brain
33	chr1:212507400-212526000	Weak transcription	HSMM	muscle
34	chr1:212507600-212519200	Weak transcription	K562	blood
35	chr1:212507600-212526000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:212507800-212519200	Weak transcription	NHDF-Ad	bronchial
37	chr1:212507800-212520800	Weak transcription	Ovary	ovary
38	chr1:212507800-212526000	Weak transcription	Fetal Brain Female	brain
39	chr1:212508000-212516400	Weak transcription	Left Ventricle	heart
40	chr1:212508000-212519200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:212508000-212519200	Weak transcription	Right Ventricle	heart
42	chr1:212508000-212519200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:212508000-212520800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:212508000-212523400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:212508000-212525600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:212508000-212525800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:212508000-212525800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:212508000-212526000	Weak transcription	Brain Substantia Nigra	brain
49	chr1:212508200-212516800	Weak transcription	Fetal Lung	lung
50	chr1:212508200-212517200	Weak transcription	Brain Angular Gyrus	brain

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