Variant report

Variant	rs2178497
Chromosome Location	chr7:107278901-107278902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107272093..107274771-chr7:107278618..107280688,2	K562	blood:
2	chr7:107276878..107279537-chr7:107440788..107443692,2	K562	blood:
3	chr7:107278392..107281833-chr7:107283832..107286049,5	K562	blood:
4	chr7:107272093..107275008-chr7:107277583..107281739,5	K562	blood:
5	chr7:107277001..107279892-chr7:107283088..107285876,2	K562	blood:

Variant related genes	Relation type
ENSG00000091138	Chromatin interaction
ENSG00000225935	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1015411	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs10234355	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs10237948	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10243340	0.84[ASN][1000 genomes]
rs10245210	0.81[ASN][1000 genomes]
rs10258385	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10264412	0.83[ASN][1000 genomes]
rs10267907	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10273733	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10274041	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10276604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10281535	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11535285	0.87[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11771278	0.85[EUR][1000 genomes]
rs11977187	0.91[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12667527	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs12668402	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12673675	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs13228252	0.85[EUR][1000 genomes]
rs1468336	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1544336	0.82[ASN][1000 genomes]
rs17154091	0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs17154104	0.84[ASN][1000 genomes]
rs2023685	0.81[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2057837	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066735	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2107713	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2189839	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2222845	0.84[AMR][1000 genomes]
rs2237670	0.80[ASN][1000 genomes]
rs2237671	0.80[ASN][1000 genomes]
rs2237672	0.80[ASN][1000 genomes]
rs2237673	0.80[ASN][1000 genomes]
rs2237676	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2237677	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237678	0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2250414	0.81[ASN][1000 genomes]
rs2253146	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2253269	0.90[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2253271	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2253833	0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2293658	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2395882	0.82[ASN][1000 genomes]
rs2395883	0.84[ASN][1000 genomes]
rs2395907	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2520241	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs2520242	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs2520243	0.91[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2520245	0.91[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2520246	0.81[ASN][1000 genomes]
rs2520247	0.81[ASN][1000 genomes]
rs2520249	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2520250	0.80[ASN][1000 genomes]
rs2520256	0.80[ASN][1000 genomes]
rs2520260	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520261	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520263	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520264	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520265	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520267	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2520268	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2520269	0.90[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2520271	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520277	0.81[ASN][1000 genomes]
rs2701684	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs2701687	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs2712189	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712191	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2712193	0.81[ASN][1000 genomes]
rs2712195	0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2712196	0.81[ASN][1000 genomes]
rs2712197	0.80[ASN][1000 genomes]
rs2712199	0.80[ASN][1000 genomes]
rs2712200	0.81[ASN][1000 genomes]
rs2712201	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs2712214	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2712215	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2712224	0.82[ASN][1000 genomes]
rs2712228	0.91[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2712229	0.94[EUR][1000 genomes]
rs2807	0.88[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2808	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28687365	0.82[ASN][1000 genomes]
rs28714607	0.82[ASN][1000 genomes]
rs2894466	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2894475	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3094383	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs34325395	0.84[ASN][1000 genomes]
rs3779494	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3779495	0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3801944	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3801948	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3801954	0.82[ASN][1000 genomes]
rs4727678	0.82[ASN][1000 genomes]
rs4727679	0.82[ASN][1000 genomes]
rs4727680	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs4727681	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs4727684	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4730245	0.94[CEU][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs57452492	0.84[ASN][1000 genomes]
rs58052742	0.83[ASN][1000 genomes]
rs62482543	0.82[ASN][1000 genomes]
rs62483722	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62483723	0.82[EUR][1000 genomes]
rs62483725	0.83[ASN][1000 genomes]
rs62483727	0.85[ASN][1000 genomes]
rs67982599	0.82[ASN][1000 genomes]
rs6976607	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7778250	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7778270	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7782057	0.82[ASN][1000 genomes]
rs7786801	0.82[ASN][1000 genomes]
rs7793613	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7803102	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7806835	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7809950	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs986994	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs987391	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1028571	chr7:107114479-107299723	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539053	chr7:107114479-107299723	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2178497	BCAP29	Cis_1M	lymphoblastoid	RTeQTL
rs2178497	COG5	cis	cerebellum	SCAN
rs2178497	SLC26A5	cis	cerebellum	SCAN
rs2178497	LAP3	trans	cerebellum	SCAN
rs2178497	COG5	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107270000-107283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:107270200-107284600	Weak transcription	Adipose Nuclei	Adipose
3	chr7:107271000-107283200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:107272600-107281600	Weak transcription	Fetal Brain Male	brain
5	chr7:107278000-107279000	Enhancers	Primary B cells from cord blood	blood
6	chr7:107278600-107279200	Flanking Active TSS	GM12878-XiMat	blood
7	chr7:107278600-107279600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:107278600-107280200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr7:107278600-107280200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr7:107278800-107279000	Enhancers	Primary T cells from cord blood	blood
11	chr7:107278800-107279400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:107278800-107279400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr7:107278800-107279400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr7:107278800-107279400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:107278800-107279400	Enhancers	Dnd41	blood
16	chr7:107278800-107279600	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr7:107278800-107279600	Enhancers	Primary hematopoietic stem cells	blood
18	chr7:107278800-107279600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr7:107278800-107279600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:107278800-107279600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:107278800-107279600	Enhancers	Fetal Thymus	thymus
22	chr7:107278800-107279600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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