Variant report

Variant	rs413972
Chromosome Location	chr6:28849711-28849712
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28688047..28690834-chr6:28847432..28849865,2	K562	blood:
2	chr6:28849269..28850881-chr6:28870428..28872541,2	MCF-7	breast:
3	chr6:28839561..28841445-chr6:28847858..28849885,2	MCF-7	breast:
4	chr6:28841283..28845553-chr6:28846644..28850092,3	MCF-7	breast:
5	chr6:28834738..28837746-chr6:28847549..28850161,3	K562	blood:
6	chr6:28847771..28851189-chr6:28852484..28857224,5	MCF-7	breast:
7	chr6:28848643..28851442-chr6:28923087..28926074,2	K562	blood:
8	chr6:28831527..28833470-chr6:28848530..28850072,2	K562	blood:
9	chr6:28848147..28850932-chr6:28889713..28892018,6	MCF-7	breast:
10	chr6:28848572..28851414-chr6:28862417..28864610,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224157	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000225595	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1061625	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs172326	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1794588	0.88[ASN][1000 genomes]
rs184094	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2013652	0.86[ASN][1000 genomes]
rs209127	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209140	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209147	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs209151	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs209165	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209172	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs209177	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs209180	0.92[ASN][1000 genomes]
rs2097424	0.88[ASN][1000 genomes]
rs2148007	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2269553	0.89[ASN][1000 genomes]
rs28381661	0.85[ASN][1000 genomes]
rs28381663	0.83[ASN][1000 genomes]
rs28743260	0.85[ASN][1000 genomes]
rs2894066	0.89[ASN][1000 genomes]
rs3131067	0.82[ASN][1000 genomes]
rs3132377	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3132380	0.85[ASN][1000 genomes]
rs3135314	0.92[ASN][1000 genomes]
rs393309	0.80[ASN][1000 genomes]
rs422331	0.94[ASN][1000 genomes]
rs429369	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4484511	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6909419	0.83[ASN][1000 genomes]
rs6912843	0.84[ASN][1000 genomes]
rs743847	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7750338	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7763940	0.85[ASN][1000 genomes]
rs7769221	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7776376	0.85[ASN][1000 genomes]
rs876737	0.82[ASN][1000 genomes]
rs9257269	0.89[ASN][1000 genomes]
rs9257270	0.88[ASN][1000 genomes]
rs9257274	0.89[ASN][1000 genomes]
rs9257280	0.88[ASN][1000 genomes]
rs9257281	0.90[ASN][1000 genomes]
rs9257328	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9257395	0.80[ASN][1000 genomes]
rs929042	0.89[ASN][1000 genomes]
rs9368576	0.85[ASN][1000 genomes]
rs9378149	0.85[ASN][1000 genomes]
rs9393932	0.85[ASN][1000 genomes]
rs9393933	0.85[ASN][1000 genomes]
rs9404976	0.85[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28848000-28849800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:28848200-28850000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28848400-28849800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:28848400-28850200	Active TSS	Fetal Brain Female	brain
5	chr6:28848600-28850000	Active TSS	Brain Anterior Caudate	brain
6	chr6:28848600-28850000	Active TSS	A549	lung
7	chr6:28849000-28849800	Active TSS	Hela-S3	cervix
8	chr6:28849000-28850200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr6:28849000-28851400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:28849000-28851600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:28849200-28849800	Enhancers	Colon Smooth Muscle	Colon
12	chr6:28849200-28850000	Enhancers	Primary T cells from cord blood	blood
13	chr6:28849200-28851000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:28849200-28851200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:28849200-28852000	Enhancers	Fetal Thymus	thymus
16	chr6:28849400-28850000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:28849400-28850800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:28849400-28851000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:28849400-28851000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:28849400-28851200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:28849400-28851400	Weak transcription	Thymus	Thymus
22	chr6:28849400-28852000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:28849400-28852200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:28849400-28863000	Weak transcription	Right Atrium	heart
25	chr6:28849600-28849800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:28849600-28849800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:28849600-28849800	Enhancers	HepG2	liver
28	chr6:28849600-28850200	Enhancers	K562	blood
29	chr6:28849600-28852000	Weak transcription	Fetal Intestine Small	intestine

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