Variant report

Variant	rs743549
Chromosome Location	chrX:153650639-153650640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1130929	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs12559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2051508	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]
rs2070643	0.87[JPT][hapmap]
rs2070807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2070819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2070821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2070825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2070827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2070829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2097214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2156911	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs2239469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2283762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs28602900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs4898484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4898494	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6727	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs743547	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs743548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[YRI][hapmap]
rs762514	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs7886627	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs915941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs915942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531227	chrX:152864376-153655730	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
2	esv33199	chrX:152864376-153820241	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	276 gene(s)	inside rSNPs	diseases
3	nsv528291	chrX:152864376-153827637	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	277 gene(s)	inside rSNPs	diseases
4	nsv915605	chrX:153333946-153783638	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
5	nsv519042	chrX:153348431-153829693	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription 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 miRNA target site	207 gene(s)	inside rSNPs	diseases
6	nsv532962	chrX:153564946-153870337	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	199 gene(s)	inside rSNPs	diseases
7	nsv532963	chrX:153576890-153822717	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	195 gene(s)	inside rSNPs	diseases
8	nsv530281	chrX:153622940-153783184	Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
9	nsv532964	chrX:153622940-153854307	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs743549	DNASE1L1	cis	multi-tissue	Pritchard
rs743549	FAM50A	cis	lymphoblastoid	seeQTL
rs743549	LILRA3	trans	lymphoblastoid	seeQTL
rs743549	PLXNA3	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153640400-153656400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chrX:153640400-153656400	Weak transcription	Small Intestine	intestine
3	chrX:153640600-153656200	Weak transcription	Fetal Kidney	kidney
4	chrX:153640600-153656600	Weak transcription	Aorta	Aorta
5	chrX:153640800-153656600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chrX:153641000-153655600	Weak transcription	Brain Cingulate Gyrus	brain
7	chrX:153641000-153656800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chrX:153641200-153656400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chrX:153641200-153656400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chrX:153641400-153655200	Weak transcription	Duodenum Mucosa	Duodenum
11	chrX:153641400-153655600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chrX:153641400-153655600	Weak transcription	Liver	Liver
13	chrX:153641400-153656200	Weak transcription	Brain Hippocampus Middle	brain
14	chrX:153641400-153656200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chrX:153641400-153656400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chrX:153641400-153656400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chrX:153641400-153656400	Weak transcription	Osteobl	bone
18	chrX:153641600-153652800	Weak transcription	Primary hematopoietic stem cells	blood
19	chrX:153641600-153655200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chrX:153641600-153655400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chrX:153641600-153655600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chrX:153641600-153655600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chrX:153641600-153656400	Weak transcription	Primary B cells from cord blood	blood
24	chrX:153641600-153656400	Weak transcription	Esophagus	oesophagus
25	chrX:153641800-153655400	Weak transcription	Pancreas	Pancrea
26	chrX:153641800-153656200	Weak transcription	Primary B cells from peripheral blood	blood
27	chrX:153641800-153656200	Weak transcription	A549	lung
28	chrX:153642400-153656200	Weak transcription	Brain Germinal Matrix	brain
29	chrX:153642600-153655400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chrX:153642600-153656200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chrX:153642600-153656400	Weak transcription	Primary T cells from cord blood	blood
32	chrX:153644000-153655400	Weak transcription	Fetal Lung	lung
33	chrX:153644000-153656400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chrX:153647800-153650800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chrX:153648800-153652600	Weak transcription	HUVEC	blood vessel
36	chrX:153648800-153655200	Weak transcription	Brain Angular Gyrus	brain
37	chrX:153649000-153655400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chrX:153649000-153656400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chrX:153649200-153656400	Weak transcription	Right Atrium	heart
40	chrX:153649400-153655400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chrX:153649400-153656200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chrX:153649800-153652600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chrX:153649800-153655400	Weak transcription	Right Ventricle	heart
44	chrX:153649800-153655600	Weak transcription	Fetal Thymus	thymus
45	chrX:153649800-153656400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chrX:153649800-153656400	Weak transcription	Left Ventricle	heart
47	chrX:153650000-153652200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chrX:153650000-153652600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chrX:153650000-153655200	Weak transcription	Adipose Nuclei	Adipose
50	chrX:153650000-153655200	Weak transcription	Ovary	ovary

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