Variant report

Variant	rs429369
Chromosome Location	chr6:28851908-28851909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28851004..28853039-chr6:28863239..28865119,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224157	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1061625	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs172326	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1794588	0.88[ASN][1000 genomes]
rs184094	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2013652	0.85[ASN][1000 genomes]
rs209127	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209140	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209147	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs209151	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209165	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs209172	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs209177	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs209180	0.91[ASN][1000 genomes]
rs2097424	0.87[ASN][1000 genomes]
rs2148007	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2269553	0.88[ASN][1000 genomes]
rs28381661	0.84[ASN][1000 genomes]
rs28381663	0.83[ASN][1000 genomes]
rs28743260	0.84[ASN][1000 genomes]
rs2894066	0.88[ASN][1000 genomes]
rs3131067	0.81[ASN][1000 genomes]
rs3132377	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3132380	0.84[ASN][1000 genomes]
rs3135314	0.92[ASN][1000 genomes]
rs413972	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs422331	0.94[ASN][1000 genomes]
rs4484511	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6909419	0.83[ASN][1000 genomes]
rs6912843	0.83[ASN][1000 genomes]
rs743847	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7750338	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763940	0.84[ASN][1000 genomes]
rs7769221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776376	0.84[ASN][1000 genomes]
rs876737	0.81[ASN][1000 genomes]
rs9257269	0.88[ASN][1000 genomes]
rs9257270	0.87[ASN][1000 genomes]
rs9257274	0.89[ASN][1000 genomes]
rs9257280	0.89[ASN][1000 genomes]
rs9257281	0.91[ASN][1000 genomes]
rs9257328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257395	0.81[ASN][1000 genomes]
rs929042	0.88[ASN][1000 genomes]
rs9368576	0.84[ASN][1000 genomes]
rs9378149	0.84[ASN][1000 genomes]
rs9393932	0.84[ASN][1000 genomes]
rs9393933	0.84[ASN][1000 genomes]
rs9404976	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs429369	HIST1H2AE	cis	parietal	SCAN
rs429369	RFP	cis	multi-tissue	Pritchard
rs429369	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28849200-28852000	Enhancers	Fetal Thymus	thymus
2	chr6:28849400-28852000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:28849400-28852200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:28849400-28863000	Weak transcription	Right Atrium	heart
5	chr6:28849600-28852000	Weak transcription	Fetal Intestine Small	intestine
6	chr6:28850800-28852000	Enhancers	Primary T cells fromperipheralblood	blood
7	chr6:28851000-28852000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:28851000-28852000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:28851000-28852800	Weak transcription	HepG2	liver
10	chr6:28851200-28852000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:28851200-28852000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:28851400-28852000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
13	chr6:28851600-28852000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:28851600-28852000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr6:28851600-28852000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:28851600-28852200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:28851600-28852200	Flanking Active TSS	Thymus	Thymus
18	chr6:28851800-28852000	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr6:28851800-28852000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:28851800-28852000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:28851800-28852200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr6:28851800-28852200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:28851800-28852200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr6:28851800-28852200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:28851800-28852400	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr6:28851800-28852400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr6:28851800-28852800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
28	chr6:28851800-28852800	Active TSS	GM12878-XiMat	blood
29	chr6:28851800-28853000	Flanking Active TSS	Dnd41	blood
30	chr6:28851800-28853400	Bivalent Enhancer	Primary B cells from peripheral blood	blood

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