Variant report

Variant	rs2736177
Chromosome Location	chr6:31586094-31586095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAL1	chr6:31586054-31586348	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31512760..31514376-chr6:31584752..31587624,2	MCF-7	breast:
2	chr6:31552844..31558545-chr6:31585940..31590373,6	MCF-7	breast:
3	chr6:31513053..31519210-chr6:31585987..31595406,29	K562	blood:
4	chr6:31553317..31555989-chr6:31586068..31588677,3	K562	blood:
5	chr6:31547327..31550393-chr6:31586001..31589795,6	K562	blood:
6	chr6:31507082..31511713-chr6:31583957..31591905,17	MCF-7	breast:
7	chr6:31586074..31595285-chr6:31626460..31635395,11	MCF-7	breast:
8	chr6:31586050..31587690-chr6:31877612..31880010,2	K562	blood:
9	chr6:31463054..31465910-chr6:31584426..31587425,2	K562	blood:
10	chr6:31506595..31512441-chr6:31585525..31590767,30	K562	blood:
11	chr6:31462191..31465976-chr6:31584426..31588689,4	K562	blood:

No data

Variant related genes	Relation type
PRRC2A	TF binding region
SNORA38	TF binding region
ENSG00000204435	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000204482	Chromatin interaction
ENSG00000201207	Chromatin interaction
ENSG00000265236	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000204439	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000227507	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000263020	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1043620	0.93[AMR][1000 genomes]
rs2857594	0.89[EUR][1000 genomes]
rs2857600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857609	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3115668	0.81[EUR][1000 genomes]
rs3115669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3117578	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130050	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130068	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3130071	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130487	0.80[EUR][1000 genomes]
rs3130625	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3131376	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3131377	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9267551	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9267576	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS 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	326 gene(s)	inside rSNPs	diseases
14	nsv462871	chr6:31575276-31632134	Strong transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
15	nsv601942	chr6:31575276-31632134	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
16	nsv884419	chr6:31585000-31632651	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	138 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2736177	HLA-DRB5	cis	lymphoblastoid	GTEx
rs2736177	HLA-DQB1	cis	multi-tissue	Pritchard
rs2736177	HLA-DRB1	cis	multi-tissue	Pritchard
rs2736177	HLA-C	cis	lymphoblastoid	GTEx
rs2736177	HLA-DRB5	cis	multi-tissue	Pritchard
rs2736177	HLA-DRB5	cis	brain	seeQTL
rs2736177	HLA-C	cis	multi-tissue	Pritchard
rs2736177	HCG27	cis	multi-tissue	Pritchard
rs2736177	HLA-DRB5	cis	lymphoblastoid	seeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31582200-31587800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:31583000-31587200	Weak transcription	Colonic Mucosa	Colon
3	chr6:31583000-31587600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:31583800-31587200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:31583800-31587200	Weak transcription	Right Atrium	heart
6	chr6:31583800-31587400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:31584000-31587200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:31584000-31587200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:31584000-31587200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:31584000-31587200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:31584000-31587200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:31584000-31587200	Weak transcription	Fetal Stomach	stomach
13	chr6:31584000-31587400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:31584000-31587400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:31584000-31587400	Weak transcription	Fetal Intestine Small	intestine
16	chr6:31584000-31587400	Weak transcription	Fetal Lung	lung
17	chr6:31584000-31587800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:31584200-31587200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:31584200-31587200	Weak transcription	Adipose Nuclei	Adipose
20	chr6:31584200-31587200	Weak transcription	Liver	Liver
21	chr6:31584200-31587200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:31584200-31587200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:31584200-31587200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:31584200-31587200	Weak transcription	Fetal Intestine Large	intestine
25	chr6:31584200-31587200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr6:31584200-31587200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:31584200-31587400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:31584200-31587400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:31584200-31587400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:31584200-31587400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:31584200-31587600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:31584200-31587800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:31584400-31587200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:31584400-31587200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:31584400-31587200	Weak transcription	Brain Anterior Caudate	brain
36	chr6:31584400-31587200	Weak transcription	Brain Substantia Nigra	brain
37	chr6:31584400-31587200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:31584400-31587200	Weak transcription	Fetal Muscle Leg	muscle
39	chr6:31584400-31587200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:31584400-31587200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:31584400-31587400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:31584400-31587400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:31584400-31587800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:31584600-31587200	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:31584600-31587200	Weak transcription	Placenta	Placenta
46	chr6:31584600-31587800	Weak transcription	Spleen	Spleen
47	chr6:31584800-31587000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr6:31584800-31587200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:31584800-31587200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:31584800-31587200	Weak transcription	Thymus	Thymus

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