Variant report

Variant	rs3095329
Chromosome Location	chr6:30693816-30693817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:242)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:242 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr6:30693588-30693999	SK-N-SH_RA	brain:	n/a	chr6:30693790-30693800
2	HEY1	chr6:30693405-30694062	K562	blood:	n/a	n/a
3	POLR2A	chr6:30692296-30694437	K562	blood:	n/a	n/a
4	BCL3	chr6:30692818-30694183	GM12878	blood:	n/a	n/a
5	CHD2	chr6:30692670-30694160	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr6:30693514-30693868	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:30693433-30694131	GM10847	blood:	n/a	n/a
8	PML	chr6:30692201-30694187	K562	blood:	n/a	n/a
9	BCL3	chr6:30693507-30694171	GM12878	blood:	n/a	n/a
10	YY1	chr6:30693518-30693816	GM12891	blood:	n/a	chr6:30693790-30693800
11	STAT5A	chr6:30692551-30694913	GM12878	blood:	n/a	chr6:30694805-30694819
12	POLR2A	chr6:30687742-30694690	GM12878	blood:	n/a	n/a
13	YY1	chr6:30693663-30693916	K562	blood:	n/a	chr6:30693790-30693800
14	POLR2A	chr6:30692324-30694192	HCT-116	colon:	n/a	n/a
15	MYBL2	chr6:30692662-30694182	HepG2	liver:	n/a	n/a
16	JUND	chr6:30693465-30694035	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:30690060-30695157	GM12892	blood:	n/a	n/a
18	JUND	chr6:30692960-30694353	HCT-116	colon:	n/a	chr6:30693232-30693243
19	POLR2A	chr6:30687036-30695449	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr6:30690176-30694491	HepG2	liver:	n/a	n/a
21	JUND	chr6:30693456-30694143	HepG2	liver:	n/a	n/a
22	JUND	chr6:30692671-30694211	HCT-116	colon:	n/a	chr6:30693232-30693243
23	POLR2A	chr6:30687122-30694167	H1-hESC	embryonic stem cell:	n/a	n/a
24	ZBTB33	chr6:30693497-30693962	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:30692770-30694169	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:30693154-30694777	HL-60	blood:	n/a	n/a
27	POLR2A	chr6:30692316-30694157	K562	blood:	n/a	n/a
28	POLR2A	chr6:30683610-30695318	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr6:30691230-30694189	K562	blood:	n/a	n/a
30	TEAD4	chr6:30692284-30694091	K562	blood:	n/a	n/a
31	NFATC1	chr6:30692636-30695046	GM12878	blood:	n/a	n/a
32	MBD4	chr6:30692362-30694218	HepG2	liver:	n/a	n/a
33	SIN3AK20	chr6:30693484-30694196	SK-N-SH	brain:	n/a	n/a
34	REST	chr6:30693495-30693839	A549	lung:	n/a	chr6:30693724-30693737
35	POLR2A	chr6:30693204-30694615	ProgFib	skin:	n/a	n/a
36	NFIC	chr6:30693534-30694177	GM12878	blood:	n/a	n/a
37	NFIC	chr6:30692597-30694809	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:30693427-30694196	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr6:30692324-30694533	HCT-116	colon:	n/a	n/a
40	CREB1	chr6:30693552-30693832	A549	lung:	n/a	n/a
41	POLR2A	chr6:30690156-30694752	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr6:30690112-30695297	Hela-S3	cervix:	n/a	n/a
43	SIN3AK20	chr6:30692575-30694762	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr6:30686736-30693839	K562	blood:	n/a	n/a
45	POLR2A	chr6:30687488-30695337	Hela-S3	cervix:	n/a	n/a
46	PML	chr6:30693486-30694201	MCF-7	breast:	n/a	n/a
47	USF1	chr6:30693336-30693850	A549	lung:	n/a	n/a
48	POLR2A	chr6:30692338-30695323	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr6:30692209-30696227	U87	brain:	n/a	n/a
50	GTF2F1	chr6:30693568-30693931	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30451219..30453103-chr6:30692483..30694829,2	K562	blood:
2	chr6:30691897..30694851-chr6:30760025..30762962,2	K562	blood:
3	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
4	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
5	chr6:30646432..30647241-chr6:30693199..30694158,2	K562	blood:
6	chr6:30608315..30616989-chr6:30683761..30694958,31	K562	blood:
7	chr6:30693361..30695767-chr6:30895208..30897558,2	K562	blood:
8	chr6:30692214..30695086-chr6:30900554..30903279,2	K562	blood:
9	chr11:62608638..62609358-chr6:30693377..30693999,2	Hela-S3	cervix:
10	chr6:30692018..30694762-chr6:30878588..30881246,2	K562	blood:
11	chr6:30693275..30696224-chr6:30778287..30780136,2	K562	blood:
12	chr6:30692887..30695267-chr6:30900165..30903279,3	K562	blood:
13	chr6:30623054..30625319-chr6:30693662..30695585,2	K562	blood:
14	chr6:30693700..30695786-chr6:32145434..32148332,2	MCF-7	breast:
15	chr6:30577862..30587208-chr6:30682997..30696247,43	MCF-7	breast:
16	chr6:30510952..30513795-chr6:30691840..30693915,2	K562	blood:
17	chr6:30693489..30695264-chr6:30866666..30869392,2	K562	blood:
18	chr13:41956378..41959414-chr6:30690779..30694701,5	K562	blood:
19	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
20	chr6:30447631..30450065-chr6:30691817..30695001,3	K562	blood:
21	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272540	TF binding region
ENSG00000204560	Chromatin interaction
ENSG00000204310	Chromatin interaction
ENSG00000137404	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000252761	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000214222	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000230449	Chromatin interaction
ENSG00000204308	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204564	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1064627	0.82[ASN][1000 genomes]
rs2284173	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284174	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs25527	0.99[ASN][1000 genomes]
rs3094127	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3094128	0.91[EUR][1000 genomes]
rs3095330	0.99[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3132584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270533	0.99[ASN][1000 genomes]
rs56389899	0.95[ASN][1000 genomes]
rs8233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295910	0.99[ASN][1000 genomes]
rs9501029	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' 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	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv970736	chr6:30692055-30710740	Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
9	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3095329	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3095329	BTN3A2	cis	multi-tissue	Pritchard
rs3095329	ZNF323	cis	parietal	SCAN
rs3095329	CCHCR1	cis	lymphoblastoid	seeQTL
rs3095329	HLA-A	cis	multi-tissue	Pritchard
rs3095329	TUBB	cis	multi-tissue	Pritchard
rs3095329	TUBB	Cis_1M	lymphoblastoid	RTeQTL
rs3095329	IP6K3	cis	parietal	SCAN
rs3095329	LOC647000	trans	multi-tissue	Pritchard
rs3095329	HLA-DQB1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30689400-30694000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:30689400-30694000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:30690000-30694000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
4	chr6:30690000-30709600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:30690200-30694000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
6	chr6:30690200-30699200	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:30690400-30696400	Strong transcription	Gastric	stomach
8	chr6:30690400-30709200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:30690600-30694000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:30690600-30694000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr6:30690600-30694000	Genic enhancers	Adipose Nuclei	Adipose
12	chr6:30690600-30694000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:30690600-30694200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr6:30690600-30694200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr6:30690600-30694400	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr6:30690600-30694400	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr6:30690600-30694400	Genic enhancers	Fetal Muscle Leg	muscle
18	chr6:30690600-30694600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:30690600-30698000	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr6:30690600-30698200	Strong transcription	Left Ventricle	heart
21	chr6:30690600-30698400	Strong transcription	Right Ventricle	heart
22	chr6:30690600-30701200	Strong transcription	Brain Angular Gyrus	brain
23	chr6:30690600-30703800	Strong transcription	Lung	lung
24	chr6:30690800-30694200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:30690800-30694200	Strong transcription	Small Intestine	intestine
26	chr6:30691000-30694000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:30691000-30694000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:30691000-30694000	Strong transcription	Brain Substantia Nigra	brain
29	chr6:30691000-30694000	Genic enhancers	Fetal Brain Male	brain
30	chr6:30691000-30694000	Genic enhancers	Fetal Thymus	thymus
31	chr6:30691000-30694000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
32	chr6:30691000-30695000	Genic enhancers	Osteobl	bone
33	chr6:30691000-30697800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:30691000-30698000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:30691000-30698000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:30691000-30698200	Strong transcription	Fetal Intestine Large	intestine
37	chr6:30691000-30698400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:30691000-30698400	Strong transcription	Brain Anterior Caudate	brain
39	chr6:30691000-30698400	Strong transcription	Brain Hippocampus Middle	brain
40	chr6:30691000-30703800	Strong transcription	Brain Cingulate Gyrus	brain
41	chr6:30691200-30697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:30691200-30697800	Strong transcription	Placenta	Placenta
43	chr6:30691600-30694000	Genic enhancers	NHDF-Ad	bronchial
44	chr6:30691600-30694200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:30691600-30695200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:30691600-30696200	Strong transcription	Thymus	Thymus
47	chr6:30691600-30698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:30691600-30698000	Strong transcription	Fetal Intestine Small	intestine
49	chr6:30691800-30694000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:30691800-30698000	Strong transcription	Duodenum Mucosa	Duodenum

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