Variant report

Variant	rs1757173
Chromosome Location	chr6:37486952-37486953
allele	G/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	chr6:37484939..37487595-chr6:37488924..37490992,2	MCF-7	breast:
3	chr6:37462097..37469080-chr6:37478016..37487473,13	K562	blood:
4	chr6:37481086..37482892-chr6:37484218..37487201,2	K562	blood:
5	chr6:37486519..37488969-chr6:37490130..37493160,3	K562	blood:
6	chr6:37483822..37487083-chr6:37490649..37493526,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198937	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1757169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757174	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757177	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757178	0.87[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757180	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757181	0.92[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1757183	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1776456	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1776460	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1776461	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2488540	0.80[ASN][1000 genomes]
rs2776875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776877	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776878	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2797801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2797803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711498	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4714072	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6903910	0.84[ASN][1000 genomes]
rs914347	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs914349	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1757173	RP1-153P14.8	cis	Whole Blood	GTEx
rs1757173	RP1-153P14.5	cis	lung	GTEx
rs1757173	RP1-153P14.5	cis	Whole Blood	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37484600-37487000	Weak transcription	Right Atrium	heart
2	chr6:37485200-37487400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:37486000-37487200	Enhancers	Thymus	Thymus
4	chr6:37486000-37487400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr6:37486200-37487600	Enhancers	Primary T cells from cord blood	blood
6	chr6:37486200-37487600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr6:37486200-37487800	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr6:37486200-37487800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr6:37486400-37488400	Weak transcription	Dnd41	blood
10	chr6:37486400-37488600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:37486400-37488600	Weak transcription	Fetal Brain Female	brain
12	chr6:37486400-37488800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:37486400-37490400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr6:37486400-37490800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:37486600-37487400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:37486600-37489800	Enhancers	Fetal Thymus	thymus
17	chr6:37486800-37487000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr6:37486800-37487200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:37486800-37487400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:37486800-37487600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr6:37486800-37487600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:37486800-37488600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:37486800-37488600	Weak transcription	Fetal Brain Male	brain
24	chr6:37486800-37491400	Enhancers	Primary T helper cells PMA-I stimulated	--

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