Variant report

Variant	rs11722278
Chromosome Location	chr4:76438427-76438428
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr4:76437757-76438495	K562	blood:	n/a	n/a
2	TEAD4	chr4:76437713-76438605	K562	blood:	n/a	n/a
3	HCFC1	chr4:76438148-76440349	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr4:76438236-76441446	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr4:76437697-76438500	IMR90	lung:	n/a	n/a
6	RCOR1	chr4:76437777-76438680	K562	blood:	n/a	n/a
7	MAFK	chr4:76437510-76438961	K562	blood:	n/a	chr4:76438856-76438876
8	POLR2A	chr4:76438385-76440702	IMR90	lung:	n/a	n/a
9	CEBPB	chr4:76437782-76438493	K562	blood:	n/a	n/a
10	TBL1XR1	chr4:76437593-76438568	K562	blood:	n/a	n/a
11	TEAD4	chr4:76437432-76438615	K562	blood:	n/a	n/a
12	FOS	chr4:76438190-76438473	MCF10A-Er-Src	breast:	n/a	n/a
13	EP300	chr4:76437674-76438453	K562	blood:	n/a	n/a
14	FOS	chr4:76438191-76438488	MCF10A-Er-Src	breast:	n/a	n/a
15	RCOR1	chr4:76437678-76438597	K562	blood:	n/a	n/a
16	JUND	chr4:76437783-76438521	K562	blood:	n/a	chr4:76438115-76438124 chr4:76438118-76438127 chr4:76438114-76438123 chr4:76438121-76438130 chr4:76438117-76438126 chr4:76438120-76438129 chr4:76438113-76438122 chr4:76438116-76438125
17	HCFC1	chr4:76437956-76438532	K562	blood:	n/a	n/a
18	MAZ	chr4:76437695-76438527	K562	blood:	n/a	n/a
19	MYC	chr4:76438273-76440163	MCF10A-Er-Src	breast:	n/a	n/a
20	EP300	chr4:76437662-76438487	GM12878	blood:	n/a	n/a
21	BHLHE40	chr4:76437690-76438526	K562	blood:	n/a	n/a
22	TAL1	chr4:76437352-76438627	K562	blood:	n/a	n/a
23	POLR2A	chr4:76437369-76438564	K562	blood:	n/a	n/a
24	IRF1	chr4:76437593-76440142	K562	blood:	n/a	chr4:76438121-76438135 chr4:76438292-76438309
25	CUX1	chr4:76437838-76438729	K562	blood:	n/a	n/a
26	ARID3A	chr4:76437467-76438438	K562	blood:	n/a	n/a
27	POLR2A	chr4:76438260-76440663	MCF10A-Er-Src	breast:	n/a	n/a
28	FOS	chr4:76438228-76438502	MCF10A-Er-Src	breast:	n/a	n/a
29	MYC	chr4:76437554-76438540	K562	blood:	n/a	n/a
30	FOS	chr4:76438190-76438596	MCF10A-Er-Src	breast:	n/a	n/a
31	MYC	chr4:76438204-76440121	MCF10A-Er-Src	breast:	n/a	n/a
32	NR2F2	chr4:76437401-76438525	K562	blood:	n/a	n/a
33	ZMIZ1	chr4:76437595-76438597	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:76438412-76438462	GM12891	blood:	n/a
2	chr4:76438412-76438462	LNCaP	prostate:	n/a
3	chr4:76438412-76438462	NHBE	bronchial:	n/a
4	chr4:76438412-76438462	HPAEpiC	pulmonary alveolar:	n/a
5	chr4:76438412-76438462	HEK293	kidney:	embryo
6	chr4:76438412-76438462	Hela-S3	cervix:	n/a
7	chr4:76438412-76438462	ECC-1	luminal epithelium:	n/a
8	chr4:76438412-76438462	ovcar-3	ovarian:	n/a
9	chr4:76438412-76438462	HUVEC	blood vessel:	n/a
10	chr4:76438412-76438462	NT2-D1	testis:	n/a
11	chr4:76438412-76438462	GM12878	blood:	n/a
12	chr4:76438412-76438462	HCF	heart:	n/a
13	chr4:76438412-76438462	AG04449	skin:	fetal
14	chr4:76438412-76438462	NH-A	brain:	n/a
15	chr4:76438412-76438462	T-47D	breast:	n/a
16	chr4:76438412-76438462	SK-N-SH_RA	brain:	n/a
17	chr4:76438412-76438462	PFSK-1	brain:	n/a
18	chr4:76438412-76438462	HRPEpiC	eye:	n/a
19	chr4:76438412-76438462	HEEpiC	esophagus:	n/a
20	chr4:76438412-76438462	CMK	blood:	n/a
21	chr4:76438412-76438462	K562	blood:	n/a
22	chr4:76438412-76438462	HRCEpiC	kidney:	n/a
23	chr4:76438412-76438462	SK-N-SH	brain:	n/a
24	chr4:76438412-76438462	AG04450	lung:	fetal
25	chr4:76438412-76438462	HNPCEpiC	eye:	n/a
26	chr4:76438412-76438462	GM12892	blood:	n/a
27	chr4:76438412-76438462	MCF10A-Er-Src	breast:	n/a
28	chr4:76438412-76438462	NB4	blood:	n/a
29	chr4:76438412-76438462	Caco-2	colon:	n/a
30	chr4:76438412-76438462	MCF-7	breast:	n/a
31	chr4:76438412-76438462	HepG2	liver:	n/a
32	chr4:76438412-76438462	SK-N-MC	brain:	n/a
33	chr4:76438412-76438462	HCT-116	colon:	n/a
34	chr4:76438412-76438462	RPTEC	kidney:	n/a
35	chr4:76438412-76438462	GM19239	blood:	n/a
36	chr4:76438412-76438462	HCPEpiC	choroid plexus:	n/a
37	chr4:76438412-76438462	HCM	heart:	n/a
38	chr4:76438412-76438462	Hepatocyte	liver:	n/a
39	chr4:76438412-76438462	U87	brain:	n/a
40	chr4:76438412-76438462	HIPEpiC	eye:	n/a
41	chr4:76438412-76438462	IMR90	lung:	fetal
42	chr4:76438412-76438462	BE2_C	brain:	n/a
43	chr4:76438412-76438462	AoSMC	blood vessel:	n/a
44	chr4:76438412-76438462	BJ	skin:	n/a
45	chr4:76438412-76438462	SAEC	small airway:	n/a
46	chr4:76438412-76438462	SKMC	muscle:	n/a
47	chr4:76438412-76438462	AG09309	skin:	n/a
48	chr4:76438412-76438462	HAEpiC	amniotic membrane:	n/a
49	chr4:76438412-76438462	HMEC	breast:	n/a
50	chr4:76438412-76438462	HL-60	blood:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:76432863..76437584-chr4:76437624..76440912,10	MCF-7	breast:
2	chr4:76433807..76436085-chr4:76437020..76439277,2	MCF-7	breast:
3	chr4:76436258..76441363-chr4:76597157..76599917,7	K562	blood:
4	chr4:76229171..76231861-chr4:76436993..76438920,2	MCF-7	breast:
5	chr4:76435978..76441393-chr4:76648372..76651737,6	K562	blood:
6	chr4:76437150..76439919-chr4:76648856..76651737,3	K562	blood:
7	chr4:76437052..76441363-chr4:76597688..76599751,3	K562	blood:

No data

Variant related genes	Relation type
THAP6	TF binding region
RCHY1	TF binding region
RCHY1	CpG island
THAP6	CpG island
ENSG00000138757	Chromatin interaction
ENSG00000163743	Chromatin interaction
ENSG00000138768	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10518140	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11721925	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11727806	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11729106	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11732511	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12644911	0.82[AFR][1000 genomes]
rs12648028	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648354	0.98[EUR][1000 genomes]
rs1351094	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs1493705	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs17271259	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs17271540	0.82[JPT][hapmap]
rs1904104	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2126854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306177	0.98[EUR][1000 genomes]
rs2867919	0.83[AFR][1000 genomes]
rs2903701	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs3905796	0.83[JPT][hapmap]
rs6836107	0.98[EUR][1000 genomes]
rs6845472	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6845588	0.98[EUR][1000 genomes]
rs7673610	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7683530	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11722278	RCHY1	cis	cerebellum	SCAN
rs11722278	RCHY1	cis	parietal	SCAN
rs11722278	RCHY1	Cis_1M	lymphoblastoid	RTeQTL
rs11722278	THAP6	cis	lymphoblastoid	seeQTL
rs11722278	THAP6	cis	multi-tissue	Pritchard
rs11722278	THAP6	cis	Lymphoblastoid	GTEx
rs11722278	RCHY1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:76425000-76438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:76425400-76439000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:76435600-76438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:76435800-76439000	Weak transcription	Gastric	stomach
6	chr4:76436000-76439400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr4:76436200-76438600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr4:76436200-76438600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:76436200-76439400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:76436200-76440600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:76436400-76438600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr4:76436400-76439000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr4:76436400-76439200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr4:76436600-76438600	Enhancers	Primary B cells from peripheral blood	blood
15	chr4:76436600-76439200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr4:76436800-76438600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr4:76436800-76438600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr4:76436800-76438800	Flanking Active TSS	HUVEC	blood vessel
19	chr4:76436800-76438800	Flanking Active TSS	K562	blood
20	chr4:76436800-76439000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr4:76437000-76438600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:76437000-76438600	Flanking Active TSS	Hela-S3	cervix
23	chr4:76437000-76438800	Flanking Active TSS	Thymus	Thymus
24	chr4:76437000-76438800	Enhancers	Spleen	Spleen
25	chr4:76437000-76439000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:76437000-76439000	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr4:76437000-76439000	Flanking Active TSS	Dnd41	blood
28	chr4:76437000-76439200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr4:76437000-76439200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:76437000-76439200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr4:76437000-76439400	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr4:76437000-76439400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:76437000-76439600	Active TSS	Right Atrium	heart
34	chr4:76437000-76440600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:76437000-76440800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:76437200-76438600	Flanking Active TSS	Fetal Heart	heart
37	chr4:76437200-76438600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr4:76437200-76438800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:76437200-76438800	Flanking Active TSS	Fetal Lung	lung
40	chr4:76437200-76439200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:76437200-76439200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr4:76437400-76438600	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr4:76437400-76438800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:76437400-76439000	Flanking Active TSS	NH-A	brain
45	chr4:76437400-76440200	Active TSS	Stomach Smooth Muscle	stomach
46	chr4:76437400-76440600	Active TSS	Psoas Muscle	Psoas
47	chr4:76437400-76440800	Active TSS	A549	lung
48	chr4:76437600-76438800	Flanking Active TSS	Fetal Thymus	thymus
49	chr4:76437600-76439200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:76437600-76440200	Active TSS	Breast Myoepithelial Primary Cells	Breast

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