Variant report

Variant	rs3132587
Chromosome Location	chr6:30685066-30685067
allele	C/T
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	chr6:30684117-30685689	GM18505	blood:	n/a	n/a
2	ZNF143	chr6:30684858-30685651	GM12878	blood:	n/a	chr6:30685196-30685215 chr6:30684984-30685002
3	HDAC2	chr6:30684675-30685564	K562	blood:	n/a	n/a
4	POLR2A	chr6:30684210-30685739	K562	blood:	n/a	n/a
5	REST	chr6:30684649-30685708	HL-60	blood:	n/a	n/a
6	TAF1	chr6:30684767-30685689	H1-neurons	neurons:	n/a	n/a
7	EP300	chr6:30684880-30685595	SK-N-SH_RA	brain:	n/a	chr6:30685569-30685583 chr6:30685391-30685398 chr6:30685573-30685582
8	ATF3	chr6:30684971-30685605	K562	blood:	n/a	chr6:30685167-30685176 chr6:30685384-30685398
9	POLR2A	chr6:30684125-30685728	GM12891	blood:	n/a	n/a
10	TBP	chr6:30684442-30685739	K562	blood:	n/a	n/a
11	MAFF	chr6:30684547-30685747	K562	blood:	n/a	n/a
12	MXI1	chr6:30684526-30685772	IMR90	lung:	n/a	n/a
13	SP2	chr6:30684729-30685743	H1-hESC	embryonic stem cell:	n/a	chr6:30685165-30685180 chr6:30685108-30685131
14	GABPA	chr6:30684716-30685638	K562	blood:	n/a	chr6:30685167-30685176 chr6:30685033-30685042 chr6:30685035-30685044
15	CEBPD	chr6:30684774-30685619	HepG2	liver:	n/a	n/a
16	TEAD4	chr6:30684167-30685849	K562	blood:	n/a	n/a
17	KAP1	chr6:30684463-30685704	U2OS	brain:	n/a	n/a
18	USF1	chr6:30684845-30685670	K562	blood:	n/a	n/a
19	REST	chr6:30684840-30685727	HepG2	liver:	n/a	n/a
20	TBL1XR1	chr6:30684280-30685723	K562	blood:	n/a	n/a
21	POLR2A	chr6:30684196-30685822	MCF-7	breast:	n/a	n/a
22	GATA3	chr6:30684926-30685779	A549	lung:	n/a	chr6:30685571-30685581
23	YY1	chr6:30684528-30685827	ECC-1	luminal epithelium:	n/a	chr6:30684977-30684985 chr6:30684794-30684816 chr6:30684952-30684963 chr6:30685167-30685176 chr6:30684966-30684988
24	POLR2A	chr6:30684238-30685759	HUVEC	blood vessel:	n/a	n/a
25	E2F6	chr6:30684882-30685552	K562	blood:	n/a	chr6:30684955-30684967 chr6:30685322-30685333 chr6:30685167-30685176 chr6:30685323-30685335 chr6:30685428-30685435
26	YY1	chr6:30684404-30685861	HepG2	liver:	n/a	chr6:30684977-30684985 chr6:30684794-30684816 chr6:30684952-30684963 chr6:30685167-30685176 chr6:30684966-30684988
27	BCLAF1	chr6:30684660-30685758	GM12878	blood:	n/a	chr6:30685569-30685578
28	STAT2	chr6:30684783-30685644	K562	blood:	n/a	chr6:30685473-30685484
29	NR2F2	chr6:30684655-30685693	MCF-7	breast:	n/a	n/a
30	REST	chr6:30684792-30685659	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr6:30684295-30685763	PBDE	blood:	n/a	n/a
32	FOXM1	chr6:30684616-30685762	MCF-7	breast:	n/a	n/a
33	EGR1	chr6:30684541-30685791	HCT-116	colon:	n/a	chr6:30685308-30685318 chr6:30685166-30685176 chr6:30685309-30685322
34	RXRA	chr6:30684873-30685583	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:30684646-30685786	IMR90	lung:	n/a	n/a
36	CEBPB	chr6:30684977-30685187	HepG2	liver:	n/a	chr6:30685106-30685114
37	MTA3	chr6:30683646-30685838	GM12878	blood:	n/a	n/a
38	SP4	chr6:30684843-30685693	H1-hESC	embryonic stem cell:	n/a	chr6:30685163-30685179 chr6:30685165-30685181
39	CEBPB	chr6:30685035-30685681	A549	lung:	n/a	chr6:30685106-30685114
40	E2F6	chr6:30684232-30685621	K562	blood:	n/a	chr6:30684955-30684967 chr6:30684874-30684884 chr6:30685322-30685333 chr6:30685167-30685176 chr6:30685323-30685335 chr6:30685428-30685435
41	POLR2A	chr6:30683610-30695318	SK-N-MC	brain:	n/a	n/a
42	YY1	chr6:30684611-30685776	H1-hESC	embryonic stem cell:	n/a	chr6:30684977-30684985 chr6:30684794-30684816 chr6:30684952-30684963 chr6:30685167-30685176 chr6:30684966-30684988
43	POLR2A	chr6:30684020-30685741	GM12892	blood:	n/a	n/a
44	HEY1	chr6:30683642-30685800	K562	blood:	n/a	n/a
45	POLR2A	chr6:30684132-30685682	GM12878	blood:	n/a	n/a
46	TBP	chr6:30684709-30685681	HepG2	liver:	n/a	n/a
47	POLR2A	chr6:30684723-30685676	HepG2	liver:	n/a	n/a
48	MYC	chr6:30684440-30685683	K562	blood:	n/a	chr6:30685463-30685472
49	SIN3AK20	chr6:30684815-30685751	SK-N-SH	brain:	n/a	n/a
50	SRF	chr6:30684843-30685839	MCF-7	breast:	n/a	chr6:30684998-30685008

No.	Distal block	Cell Line	Cell type
1	chr6:30523499..30526116-chr6:30685040..30688824,4	MCF-7	breast:
2	chr6:30685058..30687209-chr6:30852136..30853794,2	MCF-7	breast:
3	chr6:30613134..30616889-chr6:30684889..30690956,7	MCF-7	breast:
4	chr6:30482934..30485578-chr6:30684677..30686611,2	K562	blood:
5	chr17:73775360..73776254-chr6:30684520..30685811,3	Hela-S3	cervix:
6	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
7	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
8	chr6:30608315..30616989-chr6:30683761..30694958,31	K562	blood:
9	chr6:30684320..30686534-chr6:30879167..30882068,2	MCF-7	breast:
10	chr6:30683909..30686000-chr6:31586796..31589035,2	MCF-7	breast:
11	chr6:30577862..30587208-chr6:30682997..30696247,43	MCF-7	breast:
12	chr6:30455852..30458015-chr6:30684660..30687891,3	K562	blood:
13	chr6:30683565..30685674-chr6:30879957..30882271,2	K562	blood:
14	chr6:30682386..30686066-chr6:30878897..30882722,4	K562	blood:
15	chr6:30538279..30540737-chr6:30682674..30685473,2	K562	blood:
16	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
17	chr6:30658243..30658855-chr6:30684681..30685476,2	NB4	blood:
18	chr6:30683784..30686577-chr6:30843156..30844763,2	K562	blood:
19	chr1:27226461..27227347-chr6:30684694..30685447,2	Hela-S3	cervix:
20	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:

Variant related genes	Relation type
TUBB	TF binding region
MDC1	TF binding region
ENSG00000137404	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000204592	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000230449	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000198746	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000090273	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000204574	Chromatin interaction
ENSG00000235781	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs3094092	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094124	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129996	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3130000	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3130040	0.92[AMR][1000 genomes]
rs3130245	0.85[AMR][1000 genomes]
rs3132611	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9262081	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3132587	HCG22	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30683800-30686800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:30684000-30686200	Active TSS	K562	blood
3	chr6:30684200-30685800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:30684200-30685800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:30684200-30685800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:30684200-30685800	Active TSS	Brain Substantia Nigra	brain
7	chr6:30684200-30685800	Active TSS	Colon Smooth Muscle	Colon
8	chr6:30684200-30686000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:30684200-30686200	Active TSS	Fetal Brain Female	brain
10	chr6:30684200-30686400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:30684200-30686800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:30684400-30685600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:30684400-30685600	Active TSS	NHLF	lung
14	chr6:30684400-30685800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:30684400-30685800	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr6:30684400-30685800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:30684400-30686000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:30684400-30686400	Active TSS	H1 Cell Line	embryonic stem cell
19	chr6:30684400-30687000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:30684400-30690200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr6:30684600-30685200	Active TSS	Lung	lung
22	chr6:30684600-30685600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:30684600-30685600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:30684600-30685600	Active TSS	Gastric	stomach
25	chr6:30684600-30685800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:30684600-30685800	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr6:30684600-30685800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:30684600-30685800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:30684600-30685800	Active TSS	Muscle Satellite Cultured Cells	--
30	chr6:30684600-30685800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:30684600-30685800	Active TSS	Aorta	Aorta
32	chr6:30684600-30685800	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr6:30684600-30685800	Active TSS	Esophagus	oesophagus
34	chr6:30684600-30685800	Active TSS	Fetal Heart	heart
35	chr6:30684600-30685800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr6:30684600-30685800	Active TSS	Fetal Stomach	stomach
37	chr6:30684600-30685800	Active TSS	Ovary	ovary
38	chr6:30684600-30685800	Active TSS	Placenta Amnion	Placenta Amnion
39	chr6:30684600-30685800	Active TSS	Psoas Muscle	Psoas
40	chr6:30684600-30685800	Active TSS	Right Ventricle	heart
41	chr6:30684600-30685800	Active TSS	Stomach Mucosa	stomach
42	chr6:30684600-30685800	Active TSS	A549	lung
43	chr6:30684600-30685800	Active TSS	HSMM	muscle
44	chr6:30684600-30686000	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr6:30684600-30686000	Active TSS	Fetal Intestine Large	intestine
46	chr6:30684600-30686000	Active TSS	Fetal Kidney	kidney
47	chr6:30684600-30686400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:30684800-30685400	Active TSS	Primary monocytes fromperipheralblood	blood
49	chr6:30684800-30685400	Active TSS	Primary T cells from cord blood	blood
50	chr6:30684800-30685400	Active TSS	Duodenum Mucosa	Duodenum

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