Variant report

Variant	rs2535629
Chromosome Location	chr3:52833219-52833220
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	RAD21	chr3:52833105-52833400	HepG2	liver:	n/a	chr3:52833254-52833273
2	CTCF	chr3:52833033-52833387	H1-hESC	embryonic stem cell:	n/a	chr3:52833256-52833274
3	RAD21	chr3:52833001-52833471	H1-hESC	embryonic stem cell:	n/a	chr3:52833254-52833273
4	ZNF143	chr3:52833138-52833297	Hela-S3	cervix:	n/a	chr3:52833157-52833167
5	CTCF	chr3:52833149-52833381	Gliobla	brain:	n/a	chr3:52833256-52833274
6	CTCFL	chr3:52833120-52833302	K562	blood:	n/a	n/a
7	GABPA	chr3:52833050-52833386	H1-hESC	embryonic stem cell:	n/a	n/a
8	SMC3	chr3:52833128-52833423	GM12878	blood:	n/a	n/a
9	CTCF	chr3:52833200-52833350	MCF-7	breast:	n/a	chr3:52833256-52833274
10	CTCF	chr3:52833200-52833350	HCFaa	heart:	n/a	chr3:52833256-52833274
11	CTCF	chr3:52833200-52833350	GM12874	blood:	n/a	chr3:52833256-52833274
12	CTCF	chr3:52833176-52833353	Lung_OC	lung:	n/a	chr3:52833256-52833274
13	FOS	chr3:52832977-52833302	MCF10A-Er-Src	breast:	n/a	n/a
14	CTCF	chr3:52833162-52833394	MCF-7	breast:	n/a	chr3:52833256-52833274
15	CTCF	chr3:52833160-52833310	HEEpiC	esophagus:	n/a	chr3:52833256-52833274
16	CTCF	chr3:52833139-52833423	GM12878	blood:	n/a	chr3:52833256-52833274
17	FOS	chr3:52833010-52833289	MCF10A-Er-Src	breast:	n/a	n/a
18	CTCF	chr3:52833180-52833330	GM12875	blood:	n/a	chr3:52833256-52833274
19	CTCF	chr3:52833180-52833330	GM12878	blood:	n/a	chr3:52833256-52833274
20	CTCF	chr3:52833151-52833345	Fibrobl	skin:	n/a	chr3:52833256-52833274
21	CTCF	chr3:52833155-52833377	A549	lung:	n/a	chr3:52833256-52833274
22	CTCF	chr3:52833136-52833378	H1-hESC	embryonic stem cell:	n/a	chr3:52833256-52833274
23	CTCF	chr3:52833160-52833310	A549	lung:	n/a	chr3:52833256-52833274
24	CTCF	chr3:52833180-52833330	GM12869	blood:	n/a	chr3:52833256-52833274
25	CTCF	chr3:52833138-52833379	GM19239	blood:	n/a	chr3:52833256-52833274
26	CTCF	chr3:52833200-52833350	K562	blood:	n/a	chr3:52833256-52833274
27	CTCF	chr3:52833200-52833350	HFF-Myc	foreskin:	n/a	chr3:52833256-52833274
28	CTCF	chr3:52833175-52833341	Medullo	brain:	n/a	chr3:52833256-52833274
29	CTCF	chr3:52833140-52833290	HVMF	connective:	n/a	chr3:52833256-52833274
30	CTCF	chr3:52833200-52833350	NHEK	skin:	n/a	chr3:52833256-52833274
31	SMC3	chr3:52833172-52833418	K562	blood:	n/a	n/a
32	CTCF	chr3:52833035-52833442	H1-hESC	embryonic stem cell:	n/a	chr3:52833256-52833274
33	CTCF	chr3:52832973-52833564	SK-N-SH	brain:	n/a	chr3:52833256-52833274
34	CTCF	chr3:52833130-52833405	K562	blood:	n/a	chr3:52833256-52833274
35	CTCF	chr3:52833117-52833351	MCF-7	breast:	n/a	chr3:52833256-52833274
36	CTCF	chr3:52833141-52833383	MCF-7	breast:	n/a	chr3:52833256-52833274
37	CTCF	chr3:52833200-52833350	GM12870	blood:	n/a	chr3:52833256-52833274
38	CTCF	chr3:52833200-52833350	GM12801	blood:	n/a	chr3:52833256-52833274
39	CTCF	chr3:52833091-52833416	GM19238	blood:	n/a	chr3:52833256-52833274
40	CTCF	chr3:52833070-52833404	GM12891	blood:	n/a	chr3:52833256-52833274
41	CTCF	chr3:52833200-52833350	HA-sp	spinal cord:	n/a	chr3:52833256-52833274
42	FOS	chr3:52832974-52833273	MCF10A-Er-Src	breast:	n/a	n/a
43	CTCF	chr3:52833160-52833413	HUVEC	blood vessel:	n/a	chr3:52833256-52833274
44	CTCF	chr3:52833180-52833330	BE2_C	brain:	n/a	chr3:52833256-52833274
45	CTCF	chr3:52833180-52833330	SK-N-SH_RA	brain:	n/a	chr3:52833256-52833274
46	CTCF	chr3:52833164-52833324	LNCaP	prostate:	n/a	chr3:52833256-52833274
47	CTCF	chr3:52833200-52833350	HUVEC	blood vessel:	n/a	chr3:52833256-52833274
48	CTCF	chr3:52833034-52833362	HepG2	liver:	n/a	chr3:52833256-52833274
49	CTCF	chr3:52833180-52833330	RPTEC	kidney:	n/a	chr3:52833256-52833274
50	CTCF	chr3:52833160-52833310	GM12873	blood:	n/a	chr3:52833256-52833274

No.	Distal block	Cell Line	Cell type
1	chr3:52831758..52833558-chr3:52833637..52835171,2	K562	blood:
2	chr3:52827101..52830669-chr3:52833208..52834941,3	K562	blood:
3	chr3:52803280..52805303-chr3:52832255..52833885,2	MCF-7	breast:
4	chr3:52831117..52833454-chr3:52835406..52839409,3	K562	blood:
5	chr3:52831402..52833454-chr3:52836536..52839409,2	K562	blood:
6	chr3:52719608..52722839-chr3:52830545..52833712,3	K562	blood:

Variant related genes	Relation type
ITIH3	TF binding region
ENSG00000162267	Chromatin interaction
ENSG00000114904	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000163939	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1014969	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1029871	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1042779	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10510760	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1075653	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1076425	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10780035	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10865973	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10865974	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1108842	0.83[CHB][hapmap]
rs11130310	0.83[CHB][hapmap]
rs11130312	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11130315	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11130317	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11130323	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11177	0.83[CHB][hapmap]
rs11716747	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11717836	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12487591	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs12488461	0.81[JPT][hapmap]
rs12496634	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs12497998	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs12635140	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs13064064	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs13068293	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs13071584	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs13079063	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs13082208	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs13082960	0.82[JPT][hapmap]
rs13083798	0.83[CHB][hapmap]
rs13085895	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1561337	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1866268	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2019065	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2028216	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2071044	0.87[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap]
rs2071506	0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2071507	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2071508	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2072390	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2079929	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2083180	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2159644	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2164885	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2230535	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2239549	0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2239550	0.80[ASN][1000 genomes]
rs2239551	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2239699	0.80[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2240919	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2240920	0.80[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2268023	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2268025	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2268026	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2268027	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2270197	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2276824	0.83[CHB][hapmap]
rs2286798	0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2289247	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2289250	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2300149	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2302417	0.82[ASN][1000 genomes]
rs2336149	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2336545	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2535627	0.83[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap]
rs2710323	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs2710331	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33967311	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs34017441	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs35526119	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3617	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3733039	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3733041	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3733045	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3755798	0.82[JPT][hapmap]
rs3755799	0.80[CHD][hapmap]
rs3755806	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3774354	0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3774355	0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3774365	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3774366	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4481150	0.81[CHB][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4687548	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4687550	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4687551	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs4687552	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687638	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4687654	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6445534	0.83[CHB][hapmap]
rs6445535	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6617	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6762813	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6778329	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs678	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6792369	0.89[ASN][1000 genomes]
rs6804145	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6976	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs736408	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs746694	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7611731	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs7622694	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs7624716	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs767418	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs8906	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs9324	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9879090	0.82[CHB][hapmap]
rs9881468	0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs998909	0.82[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3452194	chr3:52832512-52836010	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined)	23453885	GWAS catalog

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2535629	PBRM1	cis	Thyroid	GTEx
rs2535629	RBM6	cis	cerebellum	SCAN
rs2535629	NEK4	cis	cerebellum	SCAN
rs2535629	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2535629	ITIH4	cis	multi-tissue	Pritchard
rs2535629	GNL3	cis	parietal	SCAN
rs2535629	ITIH4	cis	lymphoblastoid	seeQTL
rs2535629	FLJ12442	cis	multi-tissue	Pritchard
rs2535629	SEMA3G	cis	parietal	SCAN
rs2535629	MUSTN1	cis	Artery Aorta	GTEx
rs2535629	SPCS1	cis	parietal	SCAN
rs2535629	TMEM110	cis	parietal	SCAN
rs2535629	NEK4	cis	parietal	SCAN
rs2535629	NT5DC2	cis	lymphoblastoid	seeQTL
rs2535629	GNL3	cis	cerebellum	SCAN
rs2535629	GLT8D1	cis	lymphoblastoid	seeQTL
rs2535629	ITIH4-AS1	cis	Artery Aorta	GTEx
rs2535629	ITIH4	cis	parietal	SCAN
rs2535629	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52825800-52836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:52828200-52835800	Weak transcription	HSMMtube	muscle
3	chr3:52829000-52834200	Weak transcription	Brain Substantia Nigra	brain
4	chr3:52830400-52834000	Genic enhancers	HepG2	liver
5	chr3:52830400-52836400	Weak transcription	Pancreas	Pancrea
6	chr3:52830800-52835000	Genic enhancers	Liver	Liver
7	chr3:52832000-52833600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:52832800-52833600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:52833000-52833800	Weak transcription	Right Ventricle	heart
10	chr3:52833000-52833800	Weak transcription	Spleen	Spleen
11	chr3:52833000-52836200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:52833000-52836400	Weak transcription	HSMM	muscle
13	chr3:52833200-52834000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:52833200-52834000	Enhancers	Fetal Thymus	thymus
15	chr3:52833200-52835600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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