Variant report

Variant	rs3117572
Chromosome Location	chr6:31717692-31717693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31717233-31719181	PANC-1	pancreas:	n/a	n/a
2	JUND	chr6:31717463-31717788	K562	blood:	n/a	chr6:31717610-31717619
3	FOXA2	chr6:31717486-31717727	HepG2	liver:	n/a	n/a
4	FOXA1	chr6:31717421-31717812	HepG2	liver:	n/a	n/a
5	GATA3	chr6:31717524-31717885	T-47D	breast:	n/a	n/a
6	POLR2A	chr6:31717122-31719166	SK-N-MC	brain:	n/a	n/a
7	JUN	chr6:31717449-31717767	HepG2	liver:	n/a	chr6:31717610-31717619 chr6:31717609-31717622
8	POLR2A	chr6:31717135-31719198	K562	blood:	n/a	n/a
9	SIN3AK20	chr6:31717339-31718085	MCF-7	breast:	n/a	n/a
10	FOXA1	chr6:31717416-31717766	T-47D	breast:	n/a	n/a
11	POLR2A	chr6:31717643-31717807	K562	blood:	n/a	n/a
12	FOXA1	chr6:31717427-31717720	T-47D	breast:	n/a	n/a
13	JUND	chr6:31717440-31717804	HepG2	liver:	n/a	chr6:31717610-31717619
14	POLR2A	chr6:31717690-31717705	HepG2	liver:	n/a	n/a
15	GATA3	chr6:31717493-31717905	T-47D	breast:	n/a	n/a
16	FOXA1	chr6:31717409-31717755	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:31717491-31717968	PFSK-1	brain:	n/a	n/a
18	GATA3	chr6:31717366-31718064	MCF-7	breast:	n/a	n/a
19	FOXA1	chr6:31717420-31717759	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:31717623-31717702	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31715039..31718016-chr6:31863817..31867579,3	K562	blood:
2	chr6:31712951..31714634-chr6:31717603..31719135,2	MCF-7	breast:
3	chr6:31717258..31719013-chr6:31760100..31762521,2	MCF-7	breast:
4	chr6:31712086..31714995-chr6:31716083..31718162,2	MCF-7	breast:

Variant related genes	Relation type
MSH5	TF binding region
ENSG00000204394	Chromatin interaction
ENSG00000204371	Chromatin interaction
ENSG00000204410	Chromatin interaction
ENSG00000166278	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2227956	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2272592	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131384	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7451017	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9267577	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9267649	0.90[AMR][1000 genomes];0.84[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	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
12	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
13	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
14	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases
15	nsv819978	chr6:31713259-31721119	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	esv2763547	chr6:31715882-31738478	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3117572	HLA-C	cis	lymphoblastoid	GTEx
rs3117572	DDAH2	cis	multi-tissue	Pritchard
rs3117572	HLA-DRB5	cis	lymphoblastoid	GTEx
rs3117572	HLA-DRB5	cis	lymphoblastoid	seeQTL
rs3117572	HLA-DRB5	cis	parietal	SCAN
rs3117572	HLA-B	cis	Whole Blood	GTEx
rs3117572	HLA-DQB1	cis	lymphoblastoid	seeQTL
rs3117572	HLA-B	cis	Skin Sun Exposed Lower leg	GTEx
rs3117572	HLA-C	cis	Whole Blood	GTEx
rs3117572	VARS2	cis	lymphoblastoid	seeQTL
rs3117572	MICB	Cis_1M	lymphoblastoid	RTeQTL
rs3117572	ZKSCAN4	cis	cerebellum	SCAN
rs3117572	HLA-DRB5	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31707400-31724600	Weak transcription	Fetal Heart	heart
2	chr6:31708200-31733800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:31708400-31727000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:31708400-31729600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:31708400-31731000	Weak transcription	HSMMtube	muscle
6	chr6:31708400-31731200	Weak transcription	Gastric	stomach
7	chr6:31708400-31731200	Weak transcription	Lung	lung
8	chr6:31708400-31731200	Weak transcription	Right Atrium	heart
9	chr6:31708600-31728200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:31708600-31729400	Weak transcription	Fetal Lung	lung
11	chr6:31708600-31731200	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:31708600-31732000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:31708600-31734400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:31708800-31723200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:31708800-31727400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:31708800-31727600	Weak transcription	Spleen	Spleen
17	chr6:31708800-31731200	Weak transcription	Brain Anterior Caudate	brain
18	chr6:31708800-31737400	Weak transcription	Liver	Liver
19	chr6:31709000-31718200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:31709000-31719000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:31709000-31720400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:31709000-31720400	Weak transcription	NH-A	brain
23	chr6:31709000-31720400	Weak transcription	NHDF-Ad	bronchial
24	chr6:31709000-31721000	Weak transcription	Brain Substantia Nigra	brain
25	chr6:31709000-31722400	Weak transcription	Fetal Brain Male	brain
26	chr6:31709000-31726800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:31709000-31727000	Weak transcription	Primary T cells from cord blood	blood
28	chr6:31709000-31727600	Weak transcription	Colonic Mucosa	Colon
29	chr6:31709000-31738200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:31709200-31727200	Weak transcription	Brain Germinal Matrix	brain
31	chr6:31709200-31728400	Weak transcription	Stomach Mucosa	stomach
32	chr6:31709200-31737400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:31709600-31727800	Weak transcription	Hela-S3	cervix
34	chr6:31709600-31737400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr6:31709800-31718000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:31709800-31727200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr6:31710000-31731000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:31710600-31731200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:31710800-31720400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:31710800-31726400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:31710800-31731000	Weak transcription	HUVEC	blood vessel
42	chr6:31711200-31718600	Strong transcription	Dnd41	blood
43	chr6:31711200-31727600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr6:31711200-31731400	Weak transcription	Fetal Kidney	kidney
45	chr6:31711400-31726600	Weak transcription	Primary B cells from cord blood	blood
46	chr6:31712000-31726800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr6:31712200-31728000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:31712400-31718200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:31714800-31718600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:31714800-31718600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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