Variant report

Variant	rs1688631
Chromosome Location	chr6:119019064-119019065
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119012354..119023494-chr6:119027532..119033557,15	K562	blood:
2	chr6:119018692..119019285-chr6:119121454..119122042,2	MCF-7	breast:
3	chr6:119018340..119019295-chr6:119097391..119098460,8	MCF-7	breast:
4	chr6:119018074..119021442-chr6:119030163..119033540,4	K562	blood:
5	chr6:119002292..119005255-chr6:119017824..119020721,2	K562	blood:
6	chr6:119018713..119019314-chr6:119121262..119121860,2	MCF-7	breast:
7	chr6:119013493..119017016-chr6:119017311..119020424,5	K562	blood:

Variant related genes	Relation type
ENSG00000111860	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11754023	0.92[CEU][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1343287	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538996	0.86[ASN][1000 genomes]
rs17349329	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1771752	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1771755	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771756	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17825844	0.85[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1844963	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1844964	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1857312	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2046951	0.84[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2452262	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2638529	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638530	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2638532	0.85[ASN][1000 genomes]
rs2638533	0.85[ASN][1000 genomes]
rs2638541	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638544	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638545	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638550	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638551	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs2638552	0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2798325	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2798326	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2798327	0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2798328	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2798329	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs4027595	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4945624	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4946356	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55892056	0.80[ASN][1000 genomes]
rs56344535	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57237379	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60497831	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6911599	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs6937176	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72962906	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72962938	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7746210	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7764388	0.85[ASN][1000 genomes]
rs794857	0.86[ASN][1000 genomes]
rs794859	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs794861	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs902779	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9481850	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9489497	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9489504	0.84[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1025456	chr6:118669672-119058789	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1025097	chr6:118699752-119058789	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv532052	chr6:118711850-119057295	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv604556	chr6:118722589-119065365	Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
11	nsv949416	chr6:118772508-119033063	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
13	nsv604559	chr6:118786486-119113317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv1022865	chr6:118786586-119058789	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	esv1801472	chr6:119010065-119019064	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv830788	chr6:119014021-119143652	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1688631	TSPYL1	cis	parietal	SCAN
rs1688631	C6orf204	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118990600-119025400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:118999600-119021600	Weak transcription	Thymus	Thymus
3	chr6:119001000-119026000	Weak transcription	NH-A	brain
4	chr6:119002200-119026600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:119004000-119026600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:119007400-119021400	Weak transcription	Dnd41	blood
7	chr6:119008400-119022000	Weak transcription	GM12878-XiMat	blood
8	chr6:119010200-119019600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:119016000-119020000	Strong transcription	Primary B cells from cord blood	blood
10	chr6:119016000-119020400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:119016200-119020000	Strong transcription	Primary T cells from cord blood	blood
12	chr6:119016400-119022000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:119016600-119021800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:119016600-119021800	Strong transcription	Fetal Thymus	thymus
15	chr6:119017200-119026400	Weak transcription	HMEC	breast
16	chr6:119017400-119020200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:119017600-119019200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr6:119017600-119019400	Enhancers	Psoas Muscle	Psoas
19	chr6:119017800-119026000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:119018000-119019600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr6:119018400-119021600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:119018600-119019800	Enhancers	K562	blood
23	chr6:119018600-119021400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:119018800-119019400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr6:119018800-119020000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:119019000-119019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr6:119019000-119019200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr6:119019000-119019400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:119019000-119019400	Enhancers	Fetal Muscle Leg	muscle
30	chr6:119019000-119019600	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr6:119019000-119020000	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr6:119019000-119020200	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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