Variant report

Variant	rs3821005
Chromosome Location	chr2:178480405-178480406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178479419..178481320-chr2:178491408..178493665,2	K562	blood:
2	chr2:178255832..178259686-chr2:178477259..178480585,3	K562	blood:
3	chr2:178255150..178257645-chr2:178478947..178480585,3	K562	blood:
4	chr2:178406620..178408509-chr2:178480094..178481704,2	K562	blood:
5	chr2:178479040..178481545-chr2:178589525..178591056,2	K562	blood:

Variant related genes	Relation type
ENSG00000018510	Chromatin interaction
ENSG00000213963	Chromatin interaction
ENSG00000116044	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10497494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10497495	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10497498	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1106074	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap]
rs1527405	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[TSI][hapmap]
rs1527408	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[TSI][hapmap]
rs16865443	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16865444	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16865446	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16865448	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16865449	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16865452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16865453	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs16865475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16865492	0.94[JPT][hapmap]
rs16865501	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs16865508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16865509	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs16865514	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs16865524	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[TSI][hapmap]
rs2178018	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2293472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2365618	0.82[ASN][1000 genomes]
rs2695317	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3731803	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731804	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3731806	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770019	0.82[JPT][hapmap]
rs3770022	0.82[JPT][hapmap]
rs3813256	0.92[ASN][1000 genomes]
rs3821003	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3821004	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4144277	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5025339	0.82[ASN][1000 genomes]
rs58970701	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59677452	0.94[ASN][1000 genomes]
rs59963196	0.82[ASN][1000 genomes]
rs61164370	0.87[ASN][1000 genomes]
rs61425825	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61457959	0.82[ASN][1000 genomes]
rs61570618	0.82[ASN][1000 genomes]
rs6745743	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs6746845	0.94[CHB][hapmap];0.86[TSI][hapmap]
rs9288008	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762964	chr2:178416394-178481818	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3506731	chr2:178416851-178482200	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3506732	chr2:178416851-178482200	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3520312	chr2:178417102-178482200	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3520313	chr2:178417102-178482200	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	esv1815823	chr2:178479149-178489902	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3821005	LOC100130691	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178462800-178482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:178464200-178482600	Weak transcription	Psoas Muscle	Psoas
3	chr2:178464200-178482600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:178464600-178482400	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:178468400-178482800	Weak transcription	Fetal Brain Male	brain
6	chr2:178471800-178482600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:178472600-178481000	Weak transcription	Fetal Kidney	kidney
8	chr2:178476000-178481000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:178476400-178482800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:178476800-178482600	Weak transcription	HepG2	liver
11	chr2:178477400-178482600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:178477600-178482600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:178477800-178482400	Weak transcription	Brain Substantia Nigra	brain
14	chr2:178477800-178482800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:178477800-178482800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:178479600-178482600	Weak transcription	HSMM	muscle
17	chr2:178479800-178480800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:178479800-178481000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:178480000-178481000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:178480000-178482600	Weak transcription	K562	blood
21	chr2:178480000-178482800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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