Variant report

Variant	rs172326
Chromosome Location	chr6:28849790-28849791
allele	C/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
ENSG00000204713	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000225595	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1061625	0.89[ASN][1000 genomes]
rs1794588	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs184094	0.94[ASN][1000 genomes]
rs2013652	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209127	0.90[ASN][1000 genomes]
rs209140	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs209147	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209151	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs209165	0.95[ASN][1000 genomes]
rs209172	0.94[ASN][1000 genomes]
rs209177	0.95[ASN][1000 genomes]
rs209180	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2097424	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2148007	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	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131067	0.82[ASN][1000 genomes]
rs3132377	0.89[ASN][1000 genomes]
rs3132380	0.85[ASN][1000 genomes]
rs3135314	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs393309	0.80[ASN][1000 genomes]
rs413972	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs422331	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs429369	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4484511	0.92[ASN][1000 genomes]
rs6909419	0.83[ASN][1000 genomes]
rs6912843	0.84[ASN][1000 genomes]
rs743847	0.90[ASN][1000 genomes]
rs7750338	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7763940	0.85[ASN][1000 genomes]
rs7769221	0.97[AFR][1000 genomes];0.91[AMR][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];0.91[AMR][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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs172326	HIST1H2AE	cis	parietal	SCAN
rs172326	ZNF323	cis	parietal	SCAN
rs172326	ZKSCAN3	cis	cerebellum	SCAN
rs172326	ZNF187	cis	cerebellum	SCAN
rs172326	HIST1H2BH	cis	cerebellum	SCAN
rs172326	HIST1H2AE	cis	cerebellum	SCAN

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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