Variant report

Variant	rs2857602
Chromosome Location	chr6:31533378-31533379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31531244..31533520-chr6:31586649..31589505,2	K562	blood:
2	chr6:31532740..31534631-chr6:31581141..31583031,2	K562	blood:
3	chr6:31529234..31533520-chr6:31586129..31590672,6	K562	blood:
4	chr6:31527292..31529863-chr6:31532390..31534535,2	MCF-7	breast:
5	chr6:31526758..31530982-chr6:31533053..31538001,9	K562	blood:

Variant related genes	Relation type
ENSG00000204472	Chromatin interaction
ENSG00000204469	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1121800	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239704	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2516390	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516391	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516479	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523500	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2844483	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844484	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844485	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2844486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094595	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3135042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3135043	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746868	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs928815	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
4	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
5	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
6	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
7	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
8	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
9	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
10	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
11	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
12	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
13	esv2757162	chr6:31353329-31542308	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
14	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
15	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
16	nsv470809	chr6:31496915-31544189	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
17	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
18	nsv462870	chr6:31528130-31544189	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
19	nsv601941	chr6:31528130-31544189	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2857602	HLA-DRB5	cis	lymphoblastoid	GTEx
rs2857602	HLA-DRB5	cis	parietal	SCAN
rs2857602	HLA-DRB5	cis	multi-tissue	Pritchard
rs2857602	TEAD3	cis	cerebellum	SCAN
rs2857602	HIST1H3I	cis	cerebellum	SCAN
rs2857602	LST1	cis	multi-tissue	Pritchard
rs2857602	BAT1	cis	multi-tissue	Pritchard
rs2857602	HIST1H1B	cis	cerebellum	SCAN
rs2857602	DEF6	cis	parietal	SCAN
rs2857602	HLA-C	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31516000-31535800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:31527400-31535400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:31527400-31535400	Weak transcription	HepG2	liver
4	chr6:31528000-31535200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:31528200-31535600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:31528400-31535400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:31528600-31535600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:31528600-31541200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:31528800-31535600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:31529000-31535200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:31529000-31535200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:31529000-31535800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:31529000-31536600	Weak transcription	Dnd41	blood
14	chr6:31529000-31541200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:31529200-31533400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:31529200-31533600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:31529200-31534800	Weak transcription	Primary T cells from cord blood	blood
18	chr6:31529200-31534800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:31529200-31535200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:31529200-31535200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:31529200-31535400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:31529200-31535600	Weak transcription	Esophagus	oesophagus
23	chr6:31529400-31533400	Weak transcription	Brain Germinal Matrix	brain
24	chr6:31529400-31533400	Weak transcription	Fetal Stomach	stomach
25	chr6:31529400-31539800	Weak transcription	Thymus	Thymus
26	chr6:31529800-31535200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:31530000-31534800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:31530400-31534600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:31530600-31534000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:31530600-31534000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:31530600-31534800	Weak transcription	Fetal Thymus	thymus
32	chr6:31531200-31535400	Enhancers	GM12878-XiMat	blood
33	chr6:31531400-31536400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:31531600-31533800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:31531600-31535600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:31531800-31534400	Weak transcription	Primary B cells from cord blood	blood
37	chr6:31531800-31535600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:31532000-31535000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:31532000-31535200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:31532000-31535200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr6:31532000-31535400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr6:31532000-31535400	Weak transcription	Spleen	Spleen
43	chr6:31532000-31539800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:31532200-31535000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr6:31532800-31533400	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr6:31532800-31533400	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr6:31532800-31533600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr6:31533000-31533400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr6:31533000-31533400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr6:31533000-31533400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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