Variant report

Variant	rs2631740
Chromosome Location	chr4:8484106-8484107
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METTL19-1	chr4:8483997-8484166	ENSG00000205959.3

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10461079	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1357481	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1543246	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1880023	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1880024	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1916326	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1949733	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2010758	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2140337	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255501	0.86[EUR][1000 genomes]
rs2386227	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2450475	0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2631731	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2631734	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631735	0.85[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs2631736	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631742	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631743	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631744	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631746	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631756	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2631758	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2631762	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2688219	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2688223	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2688224	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2688227	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2688231	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688235	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2688242	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2688243	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2688247	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3103067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3103069	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3103070	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3103071	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3103072	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3103099	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696828	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447875	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6837429	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6845969	0.90[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6858542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs747580	0.87[YRI][hapmap]
rs868105	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs871768	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs940133	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs940134	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs940136	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[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	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2631740	RP11-689P11.2	cis	lung	GTEx
rs2631740	ACOX3	Cis_1M	lymphoblastoid	RTeQTL
rs2631740	TRMT44	cis	Nerve Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8473600-8501400	Weak transcription	Brain Substantia Nigra	brain
2	chr4:8475600-8491400	Weak transcription	Aorta	Aorta
3	chr4:8475800-8491800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:8478000-8500200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:8478200-8491400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:8478600-8490400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:8478600-8492000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:8479200-8486200	Weak transcription	Pancreas	Pancrea
9	chr4:8479200-8488400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:8479200-8501400	Weak transcription	Liver	Liver
11	chr4:8479400-8491200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:8479600-8485200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:8479600-8490800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:8479600-8490800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:8479800-8494600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:8480000-8493000	Weak transcription	Gastric	stomach
17	chr4:8480200-8486200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:8480200-8498400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:8480200-8501400	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:8480600-8484600	Weak transcription	Thymus	Thymus
21	chr4:8480600-8498200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:8480800-8497400	Weak transcription	Spleen	Spleen
23	chr4:8481200-8485000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:8481400-8484800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:8481400-8485000	Weak transcription	Right Ventricle	heart
26	chr4:8481400-8486800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:8481400-8490400	Weak transcription	Fetal Brain Female	brain
28	chr4:8481400-8490400	Weak transcription	Lung	lung
29	chr4:8481400-8490400	Weak transcription	Ovary	ovary
30	chr4:8481400-8491800	Weak transcription	Esophagus	oesophagus
31	chr4:8481400-8495200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:8481400-8496800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:8481400-8501400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:8481600-8493200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:8481800-8490600	Weak transcription	Fetal Stomach	stomach
36	chr4:8481800-8491800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:8481800-8497400	Weak transcription	Fetal Muscle Leg	muscle
38	chr4:8482200-8487800	Weak transcription	K562	blood
39	chr4:8482200-8495000	Weak transcription	Brain Germinal Matrix	brain
40	chr4:8482200-8501400	Weak transcription	Primary T cells from cord blood	blood
41	chr4:8483200-8484200	Enhancers	Placenta	Placenta
42	chr4:8483400-8484200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:8483800-8484200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:8483800-8488400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:8483800-8494400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr4:8484000-8484200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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