Variant report

Variant	rs1757178
Chromosome Location	chr6:37486310-37486311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37470263..37472144-chr6:37484814..37487547,2	K562	blood:
2	chr6:37485310..37486812-chr6:37496622..37499508,2	K562	blood:
3	chr6:37484939..37487595-chr6:37488924..37490992,2	MCF-7	breast:
4	chr6:37462097..37469080-chr6:37478016..37487473,13	K562	blood:
5	chr6:37481086..37482892-chr6:37484218..37487201,2	K562	blood:
6	chr6:37483726..37486812-chr6:37495696..37499508,4	K562	blood:
7	chr6:37483822..37487083-chr6:37490649..37493526,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198937	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12202055	0.83[ASN][1000 genomes]
rs12211110	0.87[MEX][hapmap]
rs1757169	0.84[CEU][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757171	0.83[ASW][hapmap];0.84[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757173	0.87[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757174	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1757177	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757180	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757181	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757183	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[GIH][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1757188	0.91[MEX][hapmap]
rs1776455	0.91[MEX][hapmap]
rs1776456	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1776460	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270687	0.87[MEX][hapmap]
rs2776875	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2776877	0.84[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2776878	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2797801	0.88[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2797803	0.82[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818987	0.80[ASN][1000 genomes]
rs4711498	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4714068	0.87[MEX][hapmap]
rs4714072	0.83[AMR][1000 genomes]
rs62408395	0.82[ASN][1000 genomes]
rs914347	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914348	0.83[ASN][1000 genomes]
rs914349	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[GIH][hapmap];0.98[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9369005	0.91[MEX][hapmap]

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	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1016310	chr6:37473075-37528469	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1757178	FTSJD2	cis	cerebellum	SCAN
rs1757178	C6orf129	cis	parietal	SCAN
rs1757178	RP1-153P14.8	cis	Whole Blood	GTEx
rs1757178	STK38	cis	parietal	SCAN
rs1757178	RNF8	cis	cerebellum	SCAN
rs1757178	FTSJD2	cis	parietal	SCAN
rs1757178	RP1-153P14.5	cis	lung	GTEx
rs1757178	RNF8	cis	parietal	SCAN
rs1757178	RP1-153P14.5	cis	Whole Blood	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37479000-37486400	Enhancers	Fetal Brain Female	brain
2	chr6:37479000-37486800	Enhancers	Fetal Brain Male	brain
3	chr6:37482400-37486400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr6:37483400-37486400	Enhancers	Primary hematopoietic stem cells	blood
5	chr6:37483400-37486400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:37483400-37486400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr6:37483600-37486600	Flanking Active TSS	Fetal Thymus	thymus
8	chr6:37484400-37486400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:37484400-37486600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:37484400-37486800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr6:37484600-37486400	Enhancers	Brain Germinal Matrix	brain
12	chr6:37484600-37486600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:37484600-37487000	Weak transcription	Right Atrium	heart
14	chr6:37485200-37486400	Enhancers	Duodenum Mucosa	Duodenum
15	chr6:37485200-37486400	Enhancers	Dnd41	blood
16	chr6:37485200-37486800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:37485200-37487400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:37486000-37486400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:37486000-37487200	Enhancers	Thymus	Thymus
20	chr6:37486000-37487400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr6:37486200-37486400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr6:37486200-37486600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:37486200-37486600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:37486200-37486600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:37486200-37486800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:37486200-37487600	Enhancers	Primary T cells from cord blood	blood
27	chr6:37486200-37487600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr6:37486200-37487800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr6:37486200-37487800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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