Variant report

Variant	rs9277962
Chromosome Location	chr6:33225322-33225323
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	chr6:33223992..33225518-chr6:33231313..33234297,2	MCF-7	breast:
2	chr6:33224298..33226172-chr6:33235633..33237854,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223501	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs120626	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213199	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213201	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213202	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213204	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213206	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213216	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs446735	0.93[ASN][1000 genomes]
rs456261	0.87[ASN][1000 genomes]
rs457565	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs463260	0.92[ASN][1000 genomes]
rs464865	0.92[ASN][1000 genomes]
rs469064	0.91[ASN][1000 genomes]
rs474353	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576890	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv462893	chr6:33142539-33256471	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv602830	chr6:33142539-33256471	Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
4	nsv462894	chr6:33174783-33254665	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
5	nsv602831	chr6:33174783-33254665	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9277962	HLA-DPA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33217400-33234200	Weak transcription	Small Intestine	intestine
2	chr6:33217800-33231200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:33217800-33231200	Weak transcription	Aorta	Aorta
4	chr6:33217800-33231400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:33218000-33226400	Weak transcription	Spleen	Spleen
6	chr6:33218000-33226600	Weak transcription	Ovary	ovary
7	chr6:33218000-33231200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:33218000-33231200	Weak transcription	Gastric	stomach
9	chr6:33218000-33231400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:33218000-33231600	Weak transcription	Psoas Muscle	Psoas
11	chr6:33218000-33235400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:33218000-33238800	Weak transcription	Right Atrium	heart
13	chr6:33218200-33226600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:33218200-33227200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:33218200-33231800	Weak transcription	Fetal Brain Male	brain
16	chr6:33218400-33226200	Weak transcription	Primary B cells from cord blood	blood
17	chr6:33218400-33226600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:33218400-33231200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:33218400-33231400	Weak transcription	Stomach Mucosa	stomach
20	chr6:33218400-33234200	Weak transcription	Fetal Heart	heart
21	chr6:33218600-33225600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:33218600-33226400	Weak transcription	Left Ventricle	heart
23	chr6:33218600-33226600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:33218600-33226800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:33218600-33231200	Weak transcription	A549	lung
26	chr6:33218600-33231400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:33218600-33231600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:33218600-33233200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:33218600-33234200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:33218800-33226600	Weak transcription	Brain Angular Gyrus	brain
31	chr6:33218800-33226600	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:33218800-33226800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:33218800-33226800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:33218800-33228000	Weak transcription	Fetal Brain Female	brain
35	chr6:33218800-33228000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:33218800-33228000	Weak transcription	Hela-S3	cervix
37	chr6:33218800-33230600	Weak transcription	Right Ventricle	heart
38	chr6:33218800-33232000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:33218800-33235400	Weak transcription	HUVEC	blood vessel
40	chr6:33219600-33227400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:33219800-33226200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:33219800-33226200	Weak transcription	Fetal Intestine Large	intestine
43	chr6:33219800-33226400	Weak transcription	Esophagus	oesophagus
44	chr6:33219800-33226600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr6:33219800-33227800	Weak transcription	NH-A	brain
46	chr6:33219800-33228200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:33219800-33228200	Weak transcription	HSMM	muscle
48	chr6:33219800-33230400	Weak transcription	Colonic Mucosa	Colon
49	chr6:33219800-33231200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:33220000-33225400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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