Variant report

Variant	rs13275593
Chromosome Location	chr8:68257300-68257301
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	chr8:68256543..68259078-chr8:68260057..68264184,4	MCF-7	breast:
2	chr8:68182907..68185887-chr8:68256451..68259285,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CSPP1-1	chr8:68256210-68257322	ENSG00000271966.1

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10957384	0.95[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11774715	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11779287	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11779992	0.84[ASN][1000 genomes]
rs11780094	0.87[ASN][1000 genomes]
rs11986169	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11995348	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12674570	0.83[ASN][1000 genomes]
rs12674848	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12675528	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12678025	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12678865	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12679614	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12681292	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12682412	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13253205	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13255070	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13264289	0.82[ASN][1000 genomes]
rs13267015	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13270606	0.87[EUR][1000 genomes]
rs13275826	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13280556	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1544986	0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17425781	0.80[ASN][1000 genomes]
rs1821026	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1864610	0.84[ASN][1000 genomes]
rs2008936	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs2116130	0.89[ASN][1000 genomes]
rs28640047	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34132973	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34345865	0.83[ASN][1000 genomes]
rs34711984	0.83[ASN][1000 genomes]
rs35017613	0.81[EUR][1000 genomes]
rs35480743	0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35754047	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35904049	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56186469	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57179217	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6472297	0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68086555	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6987724	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6992604	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6993324	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7002191	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7002622	0.81[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs7013561	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs718348	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72654960	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7464980	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7812777	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7812887	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7813810	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7817641	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7820370	0.89[ASN][1000 genomes]
rs7822637	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7823436	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7830183	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7841468	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7841756	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7844125	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7844861	0.82[ASN][1000 genomes]
rs891589	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[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	esv2752263	chr8:68170946-68788493	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv1839724	chr8:68195817-68346693	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1024135	chr8:68235792-68629789	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv539642	chr8:68235792-68629789	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv2752264	chr8:68244546-68647201	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13275593	LGALS4	trans	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:68253200-68257400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr8:68254000-68258400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr8:68254200-68257600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr8:68254200-68257800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr8:68254400-68257600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr8:68254600-68257400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr8:68254800-68257800	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr8:68256400-68257800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr8:68256600-68257800	Flanking Active TSS	Dnd41	blood
10	chr8:68256600-68258800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr8:68256600-68262400	Weak transcription	Spleen	Spleen
12	chr8:68256800-68257600	Enhancers	Primary B cells from peripheral blood	blood
13	chr8:68257000-68257400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr8:68257000-68257600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr8:68257000-68257600	Enhancers	Fetal Heart	heart
16	chr8:68257000-68257600	Enhancers	Fetal Thymus	thymus
17	chr8:68257000-68257800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr8:68257000-68257800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr8:68257000-68257800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr8:68257000-68258000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr8:68257000-68258000	Enhancers	Fetal Brain Male	brain
22	chr8:68257000-68258000	Weak transcription	Small Intestine	intestine
23	chr8:68257000-68258600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr8:68257000-68258800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr8:68257000-68258800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr8:68257000-68259000	Enhancers	Primary T cells fromperipheralblood	blood
27	chr8:68257000-68259000	Weak transcription	Fetal Muscle Leg	muscle
28	chr8:68257000-68259200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr8:68257000-68259200	Weak transcription	Thymus	Thymus
30	chr8:68257000-68259800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr8:68257000-68260400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr8:68257200-68257400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr8:68257200-68257400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr8:68257200-68257400	Enhancers	HUVEC	blood vessel
35	chr8:68257200-68257600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr8:68257200-68257600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr8:68257200-68257600	Active TSS	GM12878-XiMat	blood
38	chr8:68257200-68257800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr8:68257200-68257800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr8:68257200-68258000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr8:68257200-68258000	Weak transcription	Fetal Stomach	stomach
42	chr8:68257200-68258000	Enhancers	NHDF-Ad	bronchial
43	chr8:68257200-68258200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr8:68257200-68258200	Enhancers	Primary hematopoietic stem cells	blood
45	chr8:68257200-68258200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr8:68257200-68258600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr8:68257200-68258600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr8:68257200-68258800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr8:68257200-68259000	Weak transcription	Fetal Lung	lung
50	chr8:68257200-68259200	Weak transcription	Fetal Intestine Small	intestine

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