Variant report

Variant	rs2042995
Chromosome Location	chr2:179558366-179558367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179552876..179556381-chr2:179557098..179560477,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1001238	0.88[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs12693162	0.88[ASW][hapmap];0.88[CEU][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1560221	0.88[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs16866400	0.91[TSI][hapmap]
rs16866418	0.80[TSI][hapmap]
rs16866420	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2042996	0.94[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs2163009	0.88[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs2255167	0.97[ASN][1000 genomes]
rs2303828	0.83[TSI][hapmap]
rs2366751	0.94[ASW][hapmap];0.94[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2472751	0.94[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562834	0.80[TSI][hapmap]
rs2562845	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs2562848	0.81[MKK][hapmap]
rs2627038	0.85[MKK][hapmap]
rs36113194	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3731750	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3769864	0.94[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3813250	0.94[ASW][hapmap];0.94[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs3820978	0.80[EUR][1000 genomes]
rs3829746	0.88[ASW][hapmap];0.94[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs4894029	0.94[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs6712785	0.83[EUR][1000 genomes]
rs957875	1.00[CEU][hapmap]
rs9808377	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][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	esv2757841	chr2:179409072-179608242	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759103	chr2:179409072-179608242	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2042995	TCOF1	trans	parietal	SCAN
rs2042995	HOXD9	cis	parietal	SCAN
rs2042995	SSFA2	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179483200-179655400	Weak transcription	Adipose Nuclei	Adipose
2	chr2:179493000-179620800	Weak transcription	HSMM	muscle
3	chr2:179528200-179601200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:179528400-179563200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:179529600-179600600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:179534400-179576200	Weak transcription	Fetal Intestine Large	intestine
8	chr2:179538400-179591800	Weak transcription	Fetal Thymus	thymus
9	chr2:179540400-179586800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:179542000-179559000	Strong transcription	Fetal Heart	heart
11	chr2:179542200-179561200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:179542600-179577000	Weak transcription	Right Ventricle	heart
13	chr2:179543200-179583400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:179543400-179596800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:179544800-179579600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:179545800-179558800	Strong transcription	Primary T cells from cord blood	blood
17	chr2:179545800-179586800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:179548800-179561000	Strong transcription	HSMMtube	muscle
19	chr2:179549400-179571200	Weak transcription	GM12878-XiMat	blood
20	chr2:179551200-179558800	Strong transcription	Left Ventricle	heart
21	chr2:179552200-179560000	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:179552200-179566800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:179553000-179560800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:179553400-179570800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr2:179553600-179558800	Strong transcription	Fetal Muscle Leg	muscle
26	chr2:179554200-179566800	Weak transcription	Psoas Muscle	Psoas
27	chr2:179555000-179568800	Weak transcription	Pancreas	Pancrea
28	chr2:179555400-179558600	Strong transcription	Primary B cells from cord blood	blood
29	chr2:179556400-179566800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:179556800-179558600	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:179556800-179592200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:179557600-179559000	Strong transcription	Primary B cells from peripheral blood	blood

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