Variant report

Variant	rs3132585
Chromosome Location	chr6:30687614-30687615
allele	C/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	TAF1	chr6:30687467-30688411	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr6:30687524-30687891	U87	brain:	n/a	n/a
3	CTCF	chr6:30687580-30687730	HBMEC	blood vessel:	n/a	n/a
4	MAX	chr6:30687465-30689845	HCT-116	colon:	n/a	chr6:30689309-30689319 chr6:30689372-30689382 chr6:30689313-30689322
5	POLR2A	chr6:30687422-30690021	H1-neurons	neurons:	n/a	n/a
6	BCLAF1	chr6:30686890-30689854	GM12878	blood:	n/a	chr6:30689371-30689384 chr6:30688101-30688110
7	SIN3AK20	chr6:30687445-30688374	K562	blood:	n/a	n/a
8	CHD1	chr6:30687430-30689809	GM12878	blood:	n/a	n/a
9	SIX5	chr6:30687300-30688798	A549	lung:	n/a	chr6:30687847-30687856 chr6:30687921-30687930 chr6:30687919-30687928
10	POLR2A	chr6:30687413-30689987	HCT-116	colon:	n/a	n/a
11	CEBPB	chr6:30687183-30688260	H1-hESC	embryonic stem cell:	n/a	n/a
12	SMC3	chr6:30687490-30688251	GM12878	blood:	n/a	n/a
13	TBL1XR1	chr6:30687159-30689445	K562	blood:	n/a	n/a
14	MAX	chr6:30687507-30689656	K562	blood:	n/a	chr6:30689309-30689319 chr6:30689372-30689382 chr6:30689313-30689322
15	CREB1	chr6:30687531-30688426	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:30687036-30695449	HUVEC	blood vessel:	n/a	n/a
17	CEBPB	chr6:30687492-30688273	Hela-S3	cervix:	n/a	n/a
18	REST	chr6:30686831-30691010	H1-neurons	neurons:	n/a	chr6:30690432-30690445 chr6:30688079-30688092
19	POLR2A	chr6:30687122-30694167	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:30683610-30695318	SK-N-MC	brain:	n/a	n/a
21	RFX5	chr6:30687597-30687727	HepG2	liver:	n/a	n/a
22	CHD1	chr6:30687056-30690038	H1-hESC	embryonic stem cell:	n/a	n/a
23	RFX5	chr6:30687523-30688206	Hela-S3	cervix:	n/a	n/a
24	MAFK	chr6:30687075-30688236	H1-hESC	embryonic stem cell:	n/a	chr6:30687648-30687665
25	USF2	chr6:30687553-30688267	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr6:30687560-30687710	HMF	breast:	n/a	n/a
27	EP300	chr6:30687222-30688513	GM12878	blood:	n/a	chr6:30688056-30688072 chr6:30687483-30687497 chr6:30688359-30688373
28	ETS1	chr6:30687448-30688259	GM12878	blood:	n/a	chr6:30687918-30687931 chr6:30687917-30687930 chr6:30687922-30687929
29	CBX3	chr6:30687131-30688422	K562	blood:	n/a	n/a
30	MAX	chr6:30687495-30689914	A549	lung:	n/a	chr6:30689309-30689319 chr6:30689372-30689382 chr6:30689313-30689322
31	CTCF	chr6:30687540-30687690	HUVEC	blood vessel:	n/a	n/a
32	PML	chr6:30686897-30691157	GM12878	blood:	n/a	chr6:30687409-30687417
33	POLR2A	chr6:30687365-30689684	K562	blood:	n/a	n/a
34	YY1	chr6:30687579-30688264	SK-N-SH	brain:	n/a	n/a
35	TAF1	chr6:30687558-30689469	ECC-1	luminal epithelium:	n/a	n/a
36	CTCF	chr6:30687520-30687670	GM12878	blood:	n/a	n/a
37	MAZ	chr6:30687563-30688346	IMR90	lung:	n/a	n/a
38	POLR2A	chr6:30686736-30693839	K562	blood:	n/a	n/a
39	BACH1	chr6:30687406-30688223	H1-hESC	embryonic stem cell:	n/a	n/a
40	TBP	chr6:30687537-30689600	HepG2	liver:	n/a	n/a
41	POLR2A	chr6:30687488-30695337	Hela-S3	cervix:	n/a	n/a
42	CHD2	chr6:30687277-30688255	H1-hESC	embryonic stem cell:	n/a	n/a
43	ZNF143	chr6:30687504-30688319	GM12878	blood:	n/a	chr6:30687919-30687937 chr6:30688062-30688072 chr6:30687921-30687930 chr6:30687919-30687928
44	MXI1	chr6:30687176-30689740	GM12878	blood:	n/a	chr6:30689363-30689372
45	USF2	chr6:30687572-30688356	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr6:30687144-30689614	Raji	blood:	n/a	n/a
47	PML	chr6:30687574-30689795	K562	blood:	n/a	n/a
48	MYBL2	chr6:30687284-30689915	HepG2	liver:	n/a	n/a
49	NFIC	chr6:30687547-30688848	HepG2	liver:	n/a	n/a
50	RELA	chr6:30687085-30688330	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30687338..30691474-chr6:30850428..30854318,11	MCF-7	breast:
2	chr6:30523499..30526116-chr6:30685040..30688824,4	MCF-7	breast:
3	chr6:30629679..30632498-chr6:30687159..30689670,2	MCF-7	breast:
4	chr1:11967939..11969934-chr6:30686668..30688660,2	K562	blood:
5	chr6:30628258..30631199-chr6:30686594..30688662,2	K562	blood:
6	chr6:30613134..30616889-chr6:30684889..30690956,7	MCF-7	breast:
7	chr22:31365932..31368594-chr6:30687396..30689377,2	K562	blood:
8	chr6:30686162..30687750-chr6:30794446..30796448,2	MCF-7	breast:
9	chr6:30522151..30525852-chr6:30686505..30691954,11	K562	blood:
10	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
11	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
12	chr6:30608315..30616989-chr6:30683761..30694958,31	K562	blood:
13	chr6:30591444..30595401-chr6:30685466..30689259,5	K562	blood:
14	chr6:30538562..30540598-chr6:30686462..30688413,2	K562	blood:
15	chr6:30638422..30642374-chr6:30687329..30691225,7	MCF-7	breast:
16	chr6:30577862..30587208-chr6:30682997..30696247,43	MCF-7	breast:
17	chr6:30455852..30458015-chr6:30684660..30687891,3	K562	blood:
18	chr6:30685105..30690458-chr6:30847596..30854595,13	MCF-7	breast:
19	chr6:30590782..30598373-chr6:30685661..30690473,13	MCF-7	breast:
20	chr6:30522706..30525361-chr6:30686394..30690570,5	MCF-7	breast:
21	chr6:30455790..30458568-chr6:30687436..30691942,4	MCF-7	breast:
22	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
23	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:
24	chr6:30670013..30672002-chr6:30685618..30688068,3	MCF-7	breast:

Variant related genes	Relation type
TUBB	TF binding region
MDC1	TF binding region
ENSG00000224328	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204592	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000253352	Chromatin interaction
ENSG00000230449	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137404	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000204574	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1059612	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1264351	0.83[AMR][1000 genomes]
rs1264373	0.83[AMR][1000 genomes]
rs3094023	0.83[AMR][1000 genomes]
rs3094118	0.85[EUR][1000 genomes]
rs3094125	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3095276	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3095326	0.87[EUR][1000 genomes]
rs3095327	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3095328	0.89[EUR][1000 genomes]
rs3095332	0.89[EUR][1000 genomes]
rs3095334	0.83[EUR][1000 genomes]
rs3129972	0.90[EUR][1000 genomes]
rs3129973	0.87[EUR][1000 genomes]
rs3129974	0.89[EUR][1000 genomes]
rs3129977	0.82[EUR][1000 genomes]
rs3129978	0.83[EUR][1000 genomes]
rs3129984	0.81[EUR][1000 genomes]
rs3130117	0.83[AMR][1000 genomes]
rs3130247	0.83[AMR][1000 genomes]
rs3130658	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130660	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130665	0.85[EUR][1000 genomes]
rs3130668	0.81[EUR][1000 genomes]
rs3130673	0.83[EUR][1000 genomes]
rs3132582	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3132583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132599	0.83[EUR][1000 genomes]
rs3132600	0.87[EUR][1000 genomes]
rs3132603	0.83[EUR][1000 genomes]
rs3132605	0.83[EUR][1000 genomes]
rs9262126	0.95[EUR][1000 genomes]
rs9262130	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9262132	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9262135	0.95[EUR][1000 genomes]
rs9262141	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9262142	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9262143	0.92[EUR][1000 genomes]
rs9262146	0.83[AMR][1000 genomes];0.92[EUR][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
rs3132585	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30684400-30690200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:30684800-30688800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:30684800-30689600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:30685200-30689400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:30685600-30687800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr6:30686400-30687800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:30686600-30687800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr6:30686600-30689400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:30686600-30689400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:30686800-30687800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:30686800-30687800	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr6:30686800-30687800	Flanking Active TSS	HUVEC	blood vessel
13	chr6:30686800-30688000	Flanking Active TSS	Thymus	Thymus
14	chr6:30687000-30687800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr6:30687000-30687800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:30687000-30687800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:30687000-30687800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr6:30687000-30687800	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr6:30687000-30687800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr6:30687000-30687800	Flanking Active TSS	Fetal Thymus	thymus
21	chr6:30687000-30687800	Flanking Active TSS	NH-A	brain
22	chr6:30687000-30687800	Flanking Active TSS	NHEK	skin
23	chr6:30687000-30687800	Flanking Active TSS	Osteobl	bone
24	chr6:30687000-30689400	Active TSS	H1 Cell Line	embryonic stem cell
25	chr6:30687000-30689400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr6:30687000-30689600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:30687000-30689600	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr6:30687000-30690200	Active TSS	GM12878-XiMat	blood
29	chr6:30687000-30690400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr6:30687200-30687800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr6:30687200-30687800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr6:30687200-30687800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:30687200-30687800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:30687200-30687800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr6:30687200-30687800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:30687200-30687800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr6:30687200-30687800	Flanking Active TSS	Liver	Liver
38	chr6:30687200-30687800	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr6:30687200-30687800	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr6:30687200-30687800	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr6:30687200-30687800	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr6:30687200-30687800	Flanking Active TSS	Fetal Muscle Trunk	muscle
43	chr6:30687200-30687800	Active TSS	Right Atrium	heart
44	chr6:30687200-30687800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr6:30687200-30688600	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr6:30687200-30689000	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr6:30687200-30689000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr6:30687200-30689200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:30687200-30689400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:30687200-30689400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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