Variant report

Variant	rs2291689
Chromosome Location	chr1:78031690-78031691
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	chr1:78030983..78033542-chr1:78034721..78037146,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1135921	1.00[AMR][1000 genomes]
rs11800652	1.00[CEU][hapmap]
rs11810135	1.00[CEU][hapmap]
rs12564592	1.00[CEU][hapmap]
rs12564604	1.00[CEU][hapmap]
rs12568374	1.00[CEU][hapmap]
rs12568376	1.00[CEU][hapmap]
rs12569104	1.00[CEU][hapmap]
rs1353727	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs17100655	1.00[AMR][1000 genomes]
rs17100694	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100731	0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100774	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17100781	0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100789	1.00[MEX][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs17100850	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17100941	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2047167	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2088519	1.00[AMR][1000 genomes]
rs2245189	1.00[CEU][hapmap]
rs2256679	1.00[AMR][1000 genomes]
rs2270539	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602939	1.00[MEX][hapmap]
rs2647491	0.82[ASW][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.91[YRI][hapmap]
rs2647495	1.00[AMR][1000 genomes]
rs2647513	1.00[AMR][1000 genomes]
rs2803139	1.00[AMR][1000 genomes]
rs2803144	1.00[MEX][hapmap]
rs2803149	1.00[MEX][hapmap]
rs2803154	1.00[AMR][1000 genomes]
rs2803166	1.00[AMR][1000 genomes]
rs2803167	1.00[AMR][1000 genomes]
rs2803169	1.00[AMR][1000 genomes]
rs2803170	1.00[AMR][1000 genomes]
rs3104462	1.00[AMR][1000 genomes]
rs3104463	1.00[AMR][1000 genomes]
rs3112830	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs56259955	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2291689	NEXN	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78005600-78034800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:78005800-78032400	Weak transcription	Psoas Muscle	Psoas
3	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
4	chr1:78014400-78031800	Weak transcription	Right Ventricle	heart
5	chr1:78022400-78032400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:78022600-78034000	Strong transcription	Primary T cells from cord blood	blood
7	chr1:78023200-78050200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:78023400-78046200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:78023600-78035800	Strong transcription	HSMM	muscle
10	chr1:78023800-78048800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:78024600-78048000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:78024800-78038000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:78024800-78038000	Weak transcription	Pancreas	Pancrea
14	chr1:78024800-78048400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:78024800-78071000	Weak transcription	Gastric	stomach
16	chr1:78025000-78038000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:78025400-78050600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:78025800-78033800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:78026000-78049400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr1:78026400-78048800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:78026600-78033600	Strong transcription	NHDF-Ad	bronchial
22	chr1:78026600-78035400	Strong transcription	Fetal Thymus	thymus
23	chr1:78026800-78049200	Weak transcription	Colonic Mucosa	Colon
24	chr1:78027200-78049800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:78027400-78036000	Strong transcription	Dnd41	blood
26	chr1:78027600-78031800	Weak transcription	Fetal Stomach	stomach
27	chr1:78028000-78032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:78028400-78034200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:78028400-78035600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:78028600-78054600	Weak transcription	Esophagus	oesophagus
31	chr1:78029200-78034000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:78029400-78035400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:78029400-78035600	Weak transcription	Fetal Intestine Small	intestine
34	chr1:78029400-78039800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr1:78029600-78034800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:78029800-78033600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:78029800-78038000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:78029800-78047800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:78029800-78048000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:78029800-78050600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:78030000-78033800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:78030000-78033800	Strong transcription	HUVEC	blood vessel
43	chr1:78030000-78034800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:78030000-78035000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:78030000-78048800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:78030200-78033200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr1:78030200-78034000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr1:78030200-78034000	Strong transcription	GM12878-XiMat	blood
49	chr1:78030200-78034200	Strong transcription	Osteobl	bone
50	chr1:78030200-78034600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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