Variant report

Variant	rs668438
Chromosome Location	chr6:35901378-35901379
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35892514..35894621-chr6:35899098..35901884,2	MCF-7	breast:
2	chr6:35885929..35888867-chr6:35900395..35902266,2	K562	blood:
3	chr6:35899256..35901822-chr6:35903636..35906600,2	K562	blood:
4	chr6:35891630..35894480-chr6:35901356..35902981,2	K562	blood:
5	chr6:35887589..35889852-chr6:35900841..35903233,3	MCF-7	breast:
6	chr6:35886956..35891335-chr6:35900766..35907907,8	K562	blood:

Variant related genes	Relation type
ENSG00000096063	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10484264	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1049649	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10947572	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs10947574	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10947576	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1160827	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1160828	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751893	0.84[CEU][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11755072	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11755428	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11964319	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11968149	0.81[AMR][1000 genomes]
rs12528878	0.83[EUR][1000 genomes]
rs1326752	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1326753	0.82[EUR][1000 genomes]
rs1326756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17653835	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17654270	0.83[EUR][1000 genomes]
rs17705020	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1887170	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2038962	0.81[AMR][1000 genomes]
rs2051647	0.88[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs2148533	0.83[EUR][1000 genomes]
rs2250151	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2301510	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2395638	0.82[EUR][1000 genomes]
rs2395640	0.88[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2395641	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2395643	0.81[EUR][1000 genomes]
rs2395644	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2395645	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2395646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2766521	0.80[EUR][1000 genomes]
rs2766525	0.81[EUR][1000 genomes]
rs2817023	0.82[EUR][1000 genomes]
rs2817027	0.84[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs3213580	0.86[CEU][hapmap]
rs3891863	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs3997732	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4340986	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs582526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59190698	0.83[EUR][1000 genomes]
rs595591	1.00[ASW][hapmap];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];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612262	0.80[GIH][hapmap]
rs613540	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619264	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs637661	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639421	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640867	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644229	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457857	0.82[EUR][1000 genomes]
rs6457858	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes]
rs6457859	0.81[EUR][1000 genomes]
rs6457860	0.81[EUR][1000 genomes]
rs6457862	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6457864	0.83[EUR][1000 genomes]
rs651158	0.83[GIH][hapmap]
rs657036	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659532	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs661337	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661658	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs662713	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675664	0.82[EUR][1000 genomes]
rs677937	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905144	0.81[EUR][1000 genomes]
rs6908433	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6910906	0.82[EUR][1000 genomes]
rs6911849	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6916941	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6921531	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6923015	0.88[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6923312	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6926156	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6929493	0.88[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6931888	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs6932973	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs721694	0.82[EUR][1000 genomes]
rs72919002	0.88[EUR][1000 genomes]
rs7740886	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs7744924	0.82[EUR][1000 genomes]
rs7749862	0.83[EUR][1000 genomes]
rs7752545	0.88[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs7752551	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7755600	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7758042	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7763752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7774060	0.82[EUR][1000 genomes]
rs7776342	0.81[EUR][1000 genomes]
rs880062	0.82[EUR][1000 genomes]
rs9296168	0.88[CEU][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs9462125	0.81[EUR][1000 genomes]
rs9462128	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9462131	0.82[EUR][1000 genomes]
rs9462132	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9462133	0.82[EUR][1000 genomes]
rs9462134	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9462135	0.88[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs9462136	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9462141	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9462143	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9462144	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9470111	0.80[EUR][1000 genomes]
rs9470119	0.80[EUR][1000 genomes]
rs9470120	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9470121	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9470122	0.81[EUR][1000 genomes]
rs9470123	0.81[EUR][1000 genomes]
rs9470125	0.81[EUR][1000 genomes]
rs9470126	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9470130	0.81[EUR][1000 genomes]
rs9470131	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9470136	0.82[EUR][1000 genomes]
rs9470138	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs9470139	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9470140	0.83[EUR][1000 genomes]
rs9470141	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9470142	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9470144	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs9470147	0.88[CEU][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs9470151	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9470152	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9470153	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9470154	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9470155	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470156	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470157	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470161	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470162	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470166	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9470167	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9470169	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9470172	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9470173	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' 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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs668438	SRPK1	cis	cerebellum	SCAN
rs668438	SRPK1	cis	parietal	SCAN
rs668438	CDKN1A	cis	cerebellum	SCAN
rs668438	BRPF3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35889800-35901600	Weak transcription	Psoas Muscle	Psoas
2	chr6:35890400-35930200	Weak transcription	Pancreas	Pancrea
3	chr6:35899400-35904400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:35899600-35901600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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