Variant report

Variant	rs7552291
Chromosome Location	chr1:78031994-78031995
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: 98 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1038983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11162365	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11162366	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162368	0.93[ASN][1000 genomes]
rs11162369	0.84[EUR][1000 genomes]
rs11162370	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11162372	0.86[EUR][1000 genomes]
rs11162374	0.81[ASN][1000 genomes]
rs11162378	0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11162380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs11162383	0.80[EUR][1000 genomes]
rs11162386	0.81[EUR][1000 genomes]
rs11162387	0.80[EUR][1000 genomes]
rs11578805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs12026939	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12074409	0.85[MKK][hapmap]
rs12132838	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12142671	0.94[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs12717767	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12717768	0.96[ASN][1000 genomes]
rs1389789	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs1389790	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs1565850	0.88[MKK][hapmap]
rs1565851	0.94[ASW][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1565852	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs166770	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1962523	0.89[AMR][1000 genomes]
rs203229	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs2088058	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2296227	0.80[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.83[TSI][hapmap]
rs278833	0.90[EUR][1000 genomes]
rs278834	0.85[ASN][1000 genomes]
rs278836	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278837	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs278842	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs278843	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278847	0.81[EUR][1000 genomes]
rs278848	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs278850	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs278851	0.81[ASN][1000 genomes]
rs278854	0.94[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs278855	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs278856	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs278857	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278860	0.83[CEU][hapmap];0.97[CHD][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs278863	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs278864	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3509	0.86[MEX][hapmap];0.86[AMR][1000 genomes]
rs366467	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs370335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs371076	0.94[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs3767037	0.80[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap]
rs3767038	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs4245658	0.88[ASW][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs4949658	0.88[MKK][hapmap]
rs4949661	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949816	0.94[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4949817	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4949818	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs4949822	0.80[EUR][1000 genomes]
rs574973	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs6603955	0.83[EUR][1000 genomes]
rs6603956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6603958	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6603960	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6657290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6661656	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs6670660	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6672200	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs6674638	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6687501	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs6691317	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695989	0.83[MKK][hapmap]
rs6698151	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699205	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6699311	0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs717333	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs728741	0.92[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes]
rs7521042	0.82[EUR][1000 genomes]
rs7524866	0.93[CEU][hapmap];0.83[AMR][1000 genomes]
rs7535781	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs7545175	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7545544	0.83[MKK][hapmap]
rs7546365	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.96[ASN][1000 genomes]
rs7556227	0.81[EUR][1000 genomes]
rs7556523	0.85[ASN][1000 genomes]
rs872342	0.80[CEU][hapmap];0.84[GIH][hapmap];0.96[ASN][1000 genomes]
rs962388	0.84[AMR][1000 genomes]
rs9662527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs9988619	0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7552291	PIGK	cis	parietal	SCAN
rs7552291	AK5	cis	parietal	SCAN
rs7552291	USP33	Cis_1M	lymphoblastoid	RTeQTL
rs7552291	DNAJB4	cis	parietal	SCAN

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	chr1:78022400-78032400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:78022600-78034000	Strong transcription	Primary T cells from cord blood	blood
6	chr1:78023200-78050200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:78023400-78046200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:78023600-78035800	Strong transcription	HSMM	muscle
9	chr1:78023800-78048800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:78024600-78048000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:78024800-78038000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:78024800-78038000	Weak transcription	Pancreas	Pancrea
13	chr1:78024800-78048400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:78024800-78071000	Weak transcription	Gastric	stomach
15	chr1:78025000-78038000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:78025400-78050600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:78025800-78033800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:78026000-78049400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:78026400-78048800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:78026600-78033600	Strong transcription	NHDF-Ad	bronchial
21	chr1:78026600-78035400	Strong transcription	Fetal Thymus	thymus
22	chr1:78026800-78049200	Weak transcription	Colonic Mucosa	Colon
23	chr1:78027200-78049800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:78027400-78036000	Strong transcription	Dnd41	blood
25	chr1:78028000-78032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:78028400-78034200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:78028400-78035600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:78028600-78054600	Weak transcription	Esophagus	oesophagus
29	chr1:78029200-78034000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:78029400-78035400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:78029400-78035600	Weak transcription	Fetal Intestine Small	intestine
32	chr1:78029400-78039800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:78029600-78034800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:78029800-78033600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:78029800-78038000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:78029800-78047800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:78029800-78048000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:78029800-78050600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:78030000-78033800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:78030000-78033800	Strong transcription	HUVEC	blood vessel
41	chr1:78030000-78034800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:78030000-78035000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:78030000-78048800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:78030200-78033200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr1:78030200-78034000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr1:78030200-78034000	Strong transcription	GM12878-XiMat	blood
47	chr1:78030200-78034200	Strong transcription	Osteobl	bone
48	chr1:78030200-78034600	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:78030200-78034800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:78030200-78034800	Strong transcription	Muscle Satellite Cultured Cells	--

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