Variant report

Variant	rs3823377
Chromosome Location	chr6:29944253-29944254
allele	A/C
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	MXI1	chr6:29943993-29945799	SK-N-SH	brain:	n/a	n/a
2	SMARCB1	chr6:29943854-29945318	Hela-S3	cervix:	n/a	n/a
3	MAX	chr6:29944168-29944598	MCF-7	breast:	n/a	n/a
4	CTCF	chr6:29944239-29944537	K562	blood:	n/a	n/a
5	MAX	chr6:29944171-29945332	K562	blood:	n/a	chr6:29944813-29944823
6	ELF1	chr6:29944144-29945134	GM12878	blood:	n/a	chr6:29944888-29944900
7	HEY1	chr6:29944238-29945258	HepG2	liver:	n/a	n/a
8	ZNF143	chr6:29944248-29944504	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr6:29944203-29944638	GM12878	blood:	n/a	n/a
10	JUN	chr6:29944104-29945453	K562	blood:	n/a	chr6:29944940-29944948
11	RAD21	chr6:29944244-29944549	SK-N-SH_RA	brain:	n/a	n/a
12	RAD21	chr6:29944200-29944617	HepG2	liver:	n/a	n/a
13	MAZ	chr6:29944181-29944494	HepG2	liver:	n/a	n/a
14	MAX	chr6:29944175-29945335	K562	blood:	n/a	chr6:29944813-29944823
15	POLR2A	chr6:29944117-29945429	K562	blood:	n/a	n/a
16	CTCF	chr6:29944244-29944587	IMR90	lung:	n/a	n/a
17	NRF1	chr6:29944036-29944644	SK-N-SH	brain:	n/a	n/a
18	MAZ	chr6:29944143-29945315	K562	blood:	n/a	chr6:29944813-29944823
19	RCOR1	chr6:29944196-29944570	HepG2	liver:	n/a	n/a
20	HMGN3	chr6:29944101-29945236	K562	blood:	n/a	n/a
21	CTCF	chr6:29944114-29944572	K562	blood:	n/a	n/a
22	REST	chr6:29944253-29944587	K562	blood:	n/a	chr6:29944310-29944318
23	NFIC	chr6:29944239-29944769	GM12878	blood:	n/a	n/a
24	YY1	chr6:29944207-29944628	K562	blood:	n/a	chr6:29944483-29944497 chr6:29944481-29944492
25	HNF4G	chr6:29944213-29944619	HepG2	liver:	n/a	n/a
26	SMC3	chr6:29944252-29944563	HepG2	liver:	n/a	n/a
27	MAX	chr6:29944135-29944791	A549	lung:	n/a	n/a
28	MYC	chr6:29944211-29945354	K562	blood:	n/a	chr6:29944813-29944823
29	NR2F2	chr6:29944208-29944638	K562	blood:	n/a	n/a
30	ZBTB7A	chr6:29944186-29944528	K562	blood:	n/a	n/a
31	CBX3	chr6:29944146-29945325	K562	blood:	n/a	n/a
32	TBP	chr6:29944199-29945309	K562	blood:	n/a	n/a
33	POLR2A	chr6:29944219-29945272	HepG2	liver:	n/a	n/a
34	CTCF	chr6:29944212-29944537	K562	blood:	n/a	n/a
35	POLR2A	chr6:29944190-29945261	K562	blood:	n/a	n/a
36	E2F6	chr6:29944117-29945339	K562	blood:	n/a	chr6:29944976-29944990
37	MYBL2	chr6:29944162-29945300	HepG2	liver:	n/a	n/a
38	CTCF	chr6:29944200-29944350	HAc	cerebellar:	n/a	n/a
39	HA-E2F1	chr6:29944076-29945278	MCF-7	breast:	n/a	chr6:29944976-29944990
40	RAD21	chr6:29944226-29944562	A549	lung:	n/a	n/a
41	UBTF	chr6:29944099-29945305	K562	blood:	n/a	n/a
42	RAD21	chr6:29944228-29944499	GM12878	blood:	n/a	n/a
43	POLR2A	chr6:29943863-29944648	Hela-S3	cervix:	n/a	n/a
44	MAX	chr6:29944108-29944629	HepG2	liver:	n/a	n/a
45	JUND	chr6:29944217-29945299	K562	blood:	n/a	chr6:29944940-29944948
46	POLR2A	chr6:29944250-29945023	PFSK-1	brain:	n/a	n/a
47	RAD21	chr6:29944213-29944594	SK-N-SH_RA	brain:	n/a	n/a
48	NR2F2	chr6:29944069-29945334	K562	blood:	n/a	n/a
49	RAD21	chr6:29944162-29944607	MCF-7	breast:	n/a	n/a
50	RAD21	chr6:29944149-29944622	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:29943013..29944901-chr6:29959011..29961264,2	K562	blood:
2	chr6:29855991..29858588-chr6:29944087..29945954,2	MCF-7	breast:
3	chr6:29933916..29936718-chr6:29943405..29945040,3	MCF-7	breast:
4	chr6:29943470..29945184-chr6:29952031..29954167,2	K562	blood:
5	chr6:29943907..29944444-chr6:29980894..29981449,2	MCF-7	breast:

Variant related genes	Relation type
MICD	TF binding region
HCG9	TF binding region
ENSG00000238024	Chromatin interaction
ENSG00000230521	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12193100	0.90[ASN][1000 genomes]
rs12193110	0.91[ASN][1000 genomes]
rs12195207	0.90[ASN][1000 genomes]
rs12195260	0.90[ASN][1000 genomes]
rs12202241	0.90[ASN][1000 genomes]
rs12206499	0.90[ASN][1000 genomes]
rs2071568	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2394247	0.81[ASN][1000 genomes]
rs2517685	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523935	0.80[ASN][1000 genomes]
rs2735082	0.81[ASN][1000 genomes]
rs35066870	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35159526	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3823352	0.90[ASN][1000 genomes]
rs3823353	0.90[ASN][1000 genomes]
rs3823354	0.90[ASN][1000 genomes]
rs3823355	0.90[ASN][1000 genomes]
rs3823358	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3823369	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3823374	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3823375	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41265820	0.90[ASN][1000 genomes]
rs4248141	0.82[ASN][1000 genomes]
rs4248142	0.82[ASN][1000 genomes]
rs4248143	0.83[ASN][1000 genomes]
rs4391295	0.83[ASN][1000 genomes]
rs4538750	0.83[ASN][1000 genomes]
rs4713270	0.82[ASN][1000 genomes]
rs4713279	0.86[ASN][1000 genomes]
rs4947244	0.83[ASN][1000 genomes]
rs4959010	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4959037	0.83[ASN][1000 genomes]
rs4959038	0.83[ASN][1000 genomes]
rs4959040	0.80[ASN][1000 genomes]
rs6903753	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6904029	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914900	0.81[ASN][1000 genomes]
rs6916422	0.90[ASN][1000 genomes]
rs6916451	0.90[ASN][1000 genomes]
rs6927487	0.83[ASN][1000 genomes]
rs6935024	0.83[ASN][1000 genomes]
rs6935053	0.81[ASN][1000 genomes]
rs9295825	0.86[ASN][1000 genomes]
rs9366750	0.84[ASN][1000 genomes]
rs9378141	0.84[ASN][1000 genomes]
rs9378142	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	esv1845786	chr6:29817123-29955129	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1848127	chr6:29817323-29966451	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	esv3369212	chr6:29827361-29960177	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	esv2757159	chr6:29834472-29965501	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	esv3376588	chr6:29834667-29964324	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv10810	chr6:29837465-29961415	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv870444	chr6:29842885-29949545	Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
17	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
21	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
22	esv1799283	chr6:29938777-29959935	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	esv3350882	chr6:29942373-29945471	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3823377	HCG4P6	Cis_1M	lymphoblastoid	RTeQTL
rs3823377	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs3823377	HLA.A29.1	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29935600-29944800	Weak transcription	Dnd41	blood
2	chr6:29941600-29944400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:29942600-29944400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
4	chr6:29942600-29944400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr6:29942600-29944400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
6	chr6:29942600-29945200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:29942600-29945400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:29942600-29945400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:29942800-29944400	Bivalent Enhancer	Fetal Thymus	thymus
10	chr6:29942800-29944400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr6:29942800-29944400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr6:29942800-29945400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr6:29943000-29944400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
14	chr6:29943000-29944400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:29943000-29944400	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr6:29943000-29944400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr6:29943000-29944400	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr6:29943000-29944400	Flanking Active TSS	HepG2	liver
19	chr6:29943200-29944400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
20	chr6:29943200-29945400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
21	chr6:29943200-29945400	Active TSS	Psoas Muscle	Psoas
22	chr6:29943400-29944400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr6:29943600-29944400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
24	chr6:29943600-29944400	Flanking Active TSS	Liver	Liver
25	chr6:29943600-29944400	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr6:29943600-29944400	Flanking Active TSS	Brain Substantia Nigra	brain
27	chr6:29943600-29944400	Enhancers	Spleen	Spleen
28	chr6:29943600-29944400	Flanking Active TSS	HSMMtube	muscle
29	chr6:29943600-29945200	Active TSS	Pancreas	Pancrea
30	chr6:29943800-29944400	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr6:29943800-29944400	Bivalent Enhancer	Fetal Heart	heart
32	chr6:29943800-29944400	Bivalent Enhancer	Fetal Lung	lung
33	chr6:29943800-29944400	Flanking Active TSS	Lung	lung
34	chr6:29943800-29944400	Flanking Active TSS	Hela-S3	cervix
35	chr6:29943800-29944400	Flanking Active TSS	K562	blood
36	chr6:29943800-29944400	Flanking Active TSS	NHLF	lung
37	chr6:29943800-29944600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:29943800-29944600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:29944000-29944400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:29944000-29944400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr6:29944000-29944400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:29944000-29944400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:29944000-29944400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:29944000-29944400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
45	chr6:29944000-29944400	Flanking Bivalent TSS/Enh	NHEK	skin
46	chr6:29944000-29944600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:29944000-29945000	Active TSS	Left Ventricle	heart
48	chr6:29944000-29945000	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr6:29944000-29945200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:29944000-29945200	Active TSS	Duodenum Smooth Muscle	Duodenum

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