Variant report

Variant	rs6752850
Chromosome Location	chr2:39220655-39220656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHX57-2	chr2:39220551-39220998	ENSG00000229692.1
2	lnc-DHX57-2	chr2:39220551-39220977	ENSG00000229692.3
3	lnc-DHX57-2	chr2:39220533-39220977	ENSG00000229692.3

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10153761	0.92[ASN][1000 genomes]
rs10166631	0.82[EUR][1000 genomes]
rs10166801	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10172714	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10177250	0.83[CHB][hapmap]
rs10183915	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10186762	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10192250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10194374	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10201980	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1043793	0.91[CHB][hapmap]
rs10439459	0.91[ASN][1000 genomes]
rs10779924	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124659	0.92[ASN][1000 genomes]
rs11692687	0.92[ASN][1000 genomes]
rs12471731	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12712630	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs13023273	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1377860	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1454220	0.86[ASN][1000 genomes]
rs1454221	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1454222	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1454223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1454225	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1454226	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs1454227	0.92[ASN][1000 genomes]
rs1454228	0.91[ASN][1000 genomes]
rs1470915	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1840281	0.90[ASN][1000 genomes]
rs1869513	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1869514	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1947432	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1947433	0.81[ASN][1000 genomes]
rs2060987	0.83[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2060988	0.81[JPT][hapmap]
rs2123876	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs2123879	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2123881	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs2168042	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2168044	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2278912	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278913	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2278914	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290445	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305516	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2373474	0.90[ASN][1000 genomes]
rs2373495	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2373496	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2603145	0.84[AMR][1000 genomes]
rs2888585	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs297135	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs297148	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs297149	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap]
rs297150	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs297151	1.00[CEU][hapmap]
rs297152	1.00[CEU][hapmap]
rs297153	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs297158	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs297159	1.00[CEU][hapmap]
rs297160	1.00[CEU][hapmap]
rs371745	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3765058	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs378698	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4142729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs422854	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4643520	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670269	0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4670270	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670272	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs4670901	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4670902	0.82[EUR][1000 genomes]
rs4670903	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670905	0.91[ASN][1000 genomes]
rs4670907	0.81[ASN][1000 genomes]
rs6544183	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6544184	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6544185	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs6544186	0.80[ASN][1000 genomes]
rs6544187	0.93[AMR][1000 genomes]
rs6544194	0.86[ASN][1000 genomes]
rs6544195	0.86[ASN][1000 genomes]
rs6544197	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap]
rs6704656	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6713281	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6716101	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6725356	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6725644	0.90[ASN][1000 genomes]
rs6739568	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6755527	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6756184	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7571052	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7573310	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7577088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7594644	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9309031	0.90[ASN][1000 genomes]
rs958412	0.83[AMR][1000 genomes]
rs963730	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs963731	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs9679498	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs997344	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS 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	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6752850	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39188000-39222400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:39197000-39225800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:39200800-39227800	Weak transcription	Fetal Heart	heart
4	chr2:39202000-39221800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:39202400-39225600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:39202400-39228800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:39205800-39242600	Weak transcription	Psoas Muscle	Psoas
8	chr2:39206000-39235800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:39207600-39224400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:39209200-39222400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:39209200-39224000	Strong transcription	Placenta	Placenta
12	chr2:39209800-39224400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:39210000-39232000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:39210400-39224800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:39210400-39233200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr2:39210400-39241600	Strong transcription	Adipose Nuclei	Adipose
17	chr2:39210400-39242600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:39210600-39229400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:39210600-39242400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:39210800-39224800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:39210800-39230200	Strong transcription	Dnd41	blood
22	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:39211200-39224800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:39211200-39228600	Strong transcription	HepG2	liver
25	chr2:39211400-39221200	Weak transcription	NHDF-Ad	bronchial
26	chr2:39211400-39237800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:39211600-39242000	Weak transcription	Stomach Mucosa	stomach
28	chr2:39211800-39231200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr2:39211800-39239600	Strong transcription	Fetal Intestine Large	intestine
30	chr2:39213200-39221400	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:39213200-39221800	Weak transcription	HMEC	breast
32	chr2:39213400-39220800	Weak transcription	Fetal Kidney	kidney
33	chr2:39213400-39221000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:39213400-39221200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:39213400-39222200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:39213400-39223200	Weak transcription	GM12878-XiMat	blood
37	chr2:39213400-39224000	Weak transcription	NHLF	lung
38	chr2:39213400-39225600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:39213400-39225600	Weak transcription	Brain Anterior Caudate	brain
40	chr2:39213400-39225800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:39213400-39225800	Weak transcription	Fetal Brain Female	brain
42	chr2:39213400-39225800	Weak transcription	Spleen	Spleen
43	chr2:39213400-39226400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:39213400-39226800	Weak transcription	Aorta	Aorta
45	chr2:39213400-39228000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:39213400-39228800	Weak transcription	Brain Angular Gyrus	brain
47	chr2:39213400-39234400	Weak transcription	Gastric	stomach
48	chr2:39213400-39234400	Weak transcription	NHEK	skin
49	chr2:39213400-39242200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:39213400-39242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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