Variant report

Variant	rs7659526
Chromosome Location	chr4:106621643-106621644
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106621294..106623165-chr4:106674100..106676724,2	K562	blood:
2	chr4:106616699..106623307-chr4:106623731..106631342,11	K562	blood:
3	chr4:106621555..106624339-chr4:106624780..106626817,2	K562	blood:
4	chr4:106619847..106624541-chr4:106627186..106631133,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138785	Chromatin interaction
ENSG00000138780	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10019217	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10030620	0.80[ASN][1000 genomes]
rs10049527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10516522	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11930244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11930965	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11936611	0.82[ASN][1000 genomes]
rs11942577	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs12504088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12511885	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12512339	0.90[ASN][1000 genomes]
rs12639750	0.89[YRI][hapmap]
rs13110070	0.85[ASN][1000 genomes]
rs13145251	0.83[ASN][1000 genomes]
rs17036093	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17036097	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17036102	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036158	0.92[ASN][1000 genomes]
rs17036254	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2193852	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2193853	0.92[ASN][1000 genomes]
rs2193854	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs28370551	1.00[ASN][1000 genomes]
rs28391170	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450989	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28559909	0.97[ASN][1000 genomes]
rs28698939	0.85[ASN][1000 genomes]
rs3796926	1.00[ASN][1000 genomes]
rs4235415	0.87[ASN][1000 genomes]
rs4490460	1.00[ASN][1000 genomes]
rs4698950	0.93[ASN][1000 genomes]
rs4698951	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4699192	0.85[ASN][1000 genomes]
rs4699193	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4699194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4699195	1.00[ASN][1000 genomes]
rs4699197	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4699198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs58388061	0.95[ASN][1000 genomes]
rs58914657	0.83[ASN][1000 genomes]
rs59961848	0.84[ASN][1000 genomes]
rs60774107	0.97[ASN][1000 genomes]
rs60861135	0.92[ASN][1000 genomes]
rs6817029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6820671	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825379	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6826631	0.82[ASN][1000 genomes]
rs6843771	0.82[ASN][1000 genomes]
rs7658055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7665588	0.92[ASN][1000 genomes]
rs7696836	0.85[ASN][1000 genomes]
rs7697619	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7659526	SPTLC2	trans	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106587800-106629000	Weak transcription	Lung	lung
2	chr4:106600400-106628600	Weak transcription	Colonic Mucosa	Colon
3	chr4:106600600-106628400	Weak transcription	Stomach Mucosa	stomach
4	chr4:106601200-106628400	Weak transcription	Psoas Muscle	Psoas
5	chr4:106602200-106629200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:106602400-106628600	Weak transcription	Right Ventricle	heart
7	chr4:106602600-106621800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:106602600-106622200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:106602600-106628400	Weak transcription	Fetal Heart	heart
10	chr4:106602600-106629200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:106604400-106629200	Weak transcription	Esophagus	oesophagus
12	chr4:106604400-106629200	Weak transcription	Gastric	stomach
13	chr4:106606600-106628200	Weak transcription	Hela-S3	cervix
14	chr4:106607600-106626400	Weak transcription	Small Intestine	intestine
15	chr4:106609200-106625200	Strong transcription	HSMM	muscle
16	chr4:106610400-106628800	Weak transcription	Fetal Kidney	kidney
17	chr4:106610600-106628200	Weak transcription	Fetal Brain Male	brain
18	chr4:106610600-106628600	Weak transcription	A549	lung
19	chr4:106610800-106628600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:106611400-106623600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:106611400-106627600	Weak transcription	HepG2	liver
22	chr4:106611400-106628600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:106612400-106624600	Weak transcription	NHEK	skin
24	chr4:106612600-106621800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr4:106612600-106621800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:106613600-106628600	Weak transcription	Aorta	Aorta
27	chr4:106613600-106628600	Weak transcription	Ovary	ovary
28	chr4:106614600-106628400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr4:106614800-106628200	Weak transcription	Brain Angular Gyrus	brain
30	chr4:106615000-106623000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:106615000-106628600	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:106615400-106625000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr4:106615400-106626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:106615800-106628600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:106615800-106628600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:106616000-106628400	Weak transcription	NHLF	lung
37	chr4:106616000-106628600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:106616000-106629000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:106616200-106624600	Weak transcription	HSMMtube	muscle
40	chr4:106616200-106628400	Weak transcription	Brain Germinal Matrix	brain
41	chr4:106616400-106628400	Weak transcription	Thymus	Thymus
42	chr4:106616400-106628600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr4:106616800-106628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr4:106616800-106628600	Weak transcription	NH-A	brain
45	chr4:106617200-106622400	Strong transcription	Primary B cells from cord blood	blood
46	chr4:106617400-106627600	Weak transcription	Fetal Intestine Small	intestine
47	chr4:106617400-106628600	Weak transcription	Fetal Intestine Large	intestine
48	chr4:106617400-106628800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:106617400-106629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:106617400-106629000	Weak transcription	Pancreas	Pancrea

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