Variant report

Variant	rs461964
Chromosome Location	chr6:33360574-33360575
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:61)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr6:33358825-33360593	K562	blood:	n/a	n/a
2	CHD1	chr6:33358308-33361074	IMR90	lung:	n/a	n/a
3	MAZ	chr6:33358797-33360580	IMR90	lung:	n/a	n/a
4	TEAD4	chr6:33358444-33360667	K562	blood:	n/a	n/a
5	RFX5	chr6:33358003-33360752	SK-N-SH	brain:	n/a	n/a
6	RCOR1	chr6:33358526-33360586	K562	blood:	n/a	n/a
7	JUND	chr6:33358735-33360575	K562	blood:	n/a	n/a
8	POLR2A	chr6:33358794-33361177	PFSK-1	brain:	n/a	n/a
9	MXI1	chr6:33358639-33361468	SK-N-SH	brain:	n/a	n/a
10	MYC	chr6:33358852-33360574	K562	blood:	n/a	n/a
11	MXI1	chr6:33358441-33361393	IMR90	lung:	n/a	n/a
12	POLR2A	chr6:33358614-33360612	PBDE	blood:	n/a	n/a
13	POLR2A	chr6:33358799-33360767	Hela-S3	cervix:	n/a	n/a
14	RCOR1	chr6:33358571-33360804	K562	blood:	n/a	n/a
15	NR2F2	chr6:33358512-33361007	K562	blood:	n/a	n/a
16	POLR2A	chr6:33358830-33360739	K562	blood:	n/a	n/a
17	MXI1	chr6:33358628-33361214	K562	blood:	n/a	n/a
18	POLR2A	chr6:33358889-33361243	IMR90	lung:	n/a	n/a
19	SIN3AK20	chr6:33358910-33360606	K562	blood:	n/a	n/a
20	BHLHE40	chr6:33360191-33360619	K562	blood:	n/a	n/a
21	MAX	chr6:33358683-33360589	K562	blood:	n/a	n/a
22	WRNIP1	chr6:33360531-33360617	GM12878	blood:	n/a	n/a
23	MTA3	chr6:33358347-33360985	GM12878	blood:	n/a	n/a
24	CBX3	chr6:33358441-33360640	K562	blood:	n/a	n/a
25	E2F4	chr6:33358937-33360983	MCF10A-Er-Src	breast:	n/a	n/a
26	TAL1	chr6:33360301-33360637	K562	blood:	n/a	n/a
27	PML	chr6:33358460-33360588	K562	blood:	n/a	n/a
28	HCFC1	chr6:33358279-33360947	Hela-S3	cervix:	n/a	n/a
29	EP300	chr6:33358526-33360574	K562	blood:	n/a	chr6:33359093-33359100 chr6:33360076-33360090 chr6:33359422-33359429

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33360547-33360597	HIPEpiC	eye:	n/a
2	chr6:33360547-33360597	BJ	skin:	n/a
3	chr6:33360547-33360597	AG09309	skin:	n/a
4	chr6:33360547-33360597	GM12892	blood:	n/a
5	chr6:33360547-33360597	BE2_C	brain:	n/a
6	chr6:33360547-33360597	AG09319	gingival:	n/a
7	chr6:33360547-33360597	HAEpiC	amniotic membrane:	n/a
8	chr6:33360547-33360597	GM19239	blood:	n/a
9	chr6:33360547-33360597	MCF-7	breast:	n/a
10	chr6:33360547-33360597	HMEC	breast:	n/a
11	chr6:33360547-33360597	Hepatocyte	liver:	n/a
12	chr6:33360547-33360597	Hela-S3	cervix:	n/a
13	chr6:33360547-33360597	ovcar-3	ovarian:	n/a
14	chr6:33360547-33360597	HL-60	blood:	n/a
15	chr6:33360547-33360597	PANC-1	pancreas:	n/a
16	chr6:33360547-33360597	HepG2	liver:	n/a
17	chr6:33360547-33360597	MCF10A-Er-Src	breast:	n/a
18	chr6:33360547-33360597	HPAEpiC	pulmonary alveolar:	n/a
19	chr6:33360547-33360597	HRPEpiC	eye:	n/a
20	chr6:33360547-33360597	SKMC	muscle:	n/a
21	chr6:33360547-33360597	GM12891	blood:	n/a
22	chr6:33360547-33360597	NHBE	bronchial:	n/a
23	chr6:33360547-33360597	T-47D	breast:	n/a
24	chr6:33360547-33360597	HEK293	kidney:	embryo
25	chr6:33360547-33360597	SK-N-SH	brain:	n/a
26	chr6:33360547-33360597	AG04450	lung:	fetal
27	chr6:33360547-33360597	PrEC	prostate:	n/a
28	chr6:33360547-33360597	NH-A	brain:	n/a
29	chr6:33360547-33360597	A549	lung:	n/a
30	chr6:33360547-33360597	HCPEpiC	choroid plexus:	n/a
31	chr6:33360547-33360597	AoSMC	blood vessel:	n/a
32	chr6:33360547-33360597	Caco-2	colon:	n/a
33	chr6:33360547-33360597	GM12878	blood:	n/a
34	chr6:33360547-33360597	ProgFib	skin:	n/a
35	chr6:33360547-33360597	U87	brain:	n/a
36	chr6:33360547-33360597	HRCEpiC	kidney:	n/a
37	chr6:33360547-33360597	NT2-D1	testis:	n/a
38	chr6:33360547-33360597	K562	blood:	n/a
39	chr6:33360547-33360597	CMK	blood:	n/a
40	chr6:33360547-33360597	HCM	heart:	n/a
41	chr6:33360547-33360597	HCF	heart:	n/a
42	chr6:33360547-33360597	HUVEC	blood vessel:	n/a
43	chr6:33360547-33360597	SK-N-SH_RA	brain:	n/a
44	chr6:33360547-33360597	HCT-116	colon:	n/a
45	chr6:33360547-33360597	SK-N-MC	brain:	n/a
46	chr6:33360547-33360597	GM06990	blood:	n/a
47	chr6:33360547-33360597	AG10803	skin:	n/a
48	chr6:33360547-33360597	HEEpiC	esophagus:	n/a
49	chr6:33360547-33360597	NHDF-neo	bronchial:	n/a
50	chr6:33360547-33360597	PFSK-1	brain:	n/a

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:32936666..32939842-chr6:33360330..33364086,3	MCF-7	breast:
2	chr6:33279554..33283546-chr6:33360483..33362156,3	MCF-7	breast:
3	chr6:32936394..32938328-chr6:33359727..33361307,2	K562	blood:
4	chr6:33356382..33361019-chr6:33384058..33388661,8	K562	blood:
5	chr6:33242419..33244049-chr6:33358539..33360870,2	MCF-7	breast:
6	chr6:33283316..33288344-chr6:33357863..33362367,8	K562	blood:
7	chr6:33357335..33362175-chr6:33383352..33389421,14	K562	blood:
8	chr6:33239039..33242495-chr6:33357243..33362134,5	MCF-7	breast:
9	chr6:33264068..33267385-chr6:33357975..33361447,5	MCF-7	breast:
10	chr6:33359751..33362577-chr6:33420507..33423497,2	K562	blood:
11	chr6:33358575..33362850-chr6:33383674..33386989,4	MCF-7	breast:
12	chr6:33358270..33361160-chr6:33397889..33401606,4	K562	blood:
13	chr6:33357351..33361150-chr6:33373102..33380127,12	MCF-7	breast:
14	chr6:33285348..33292496-chr6:33357328..33361566,13	K562	blood:
15	chr6:33238428..33241280-chr6:33357854..33362793,6	MCF-7	breast:
16	chr6:33241732..33243308-chr6:33359602..33361155,2	K562	blood:
17	chr6:33237283..33247485-chr6:33356185..33362256,17	K562	blood:
18	chr6:33280908..33284579-chr6:33359142..33361187,5	K562	blood:
19	chr6:33264179..33271329-chr6:33356528..33360865,9	K562	blood:
20	chr6:33256540..33259907-chr6:33358017..33361464,3	MCF-7	breast:
21	chr6:33283943..33291558-chr6:33357867..33362243,10	MCF-7	breast:
22	chr6:33243392..33248315-chr6:33357393..33361975,11	K562	blood:
23	chr6:33280708..33283139-chr6:33358214..33362149,5	K562	blood:
24	chr6:33358950..33361251-chr6:33421997..33423819,3	K562	blood:
25	chr6:33253660..33257073-chr6:33358023..33361324,4	K562	blood:
26	chr6:33356271..33363521-chr6:33371085..33380351,32	K562	blood:
27	chr6:33357884..33361160-chr6:33397889..33401606,5	K562	blood:
28	chr6:33283728..33287391-chr6:33357794..33361686,6	MCF-7	breast:
29	chr6:33265384..33269852-chr6:33356528..33361842,9	K562	blood:

No data

Variant related genes	Relation type
RPL35AP4	TF binding region
RPL35AP4	CpG island
ENSG00000223501	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000231500	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12204193	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1613451	0.82[ASN][1000 genomes]
rs1755047	0.82[ASN][1000 genomes]
rs2076775	0.82[ASN][1000 genomes]
rs211456	0.80[ASN][1000 genomes]
rs2247385	0.81[ASN][1000 genomes]
rs2274730	0.87[ASN][1000 genomes]
rs2480487	0.81[ASN][1000 genomes]
rs2743	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2747477	0.83[ASN][1000 genomes]
rs2747479	0.83[ASN][1000 genomes]
rs2772373	0.84[ASN][1000 genomes]
rs2772376	0.81[ASN][1000 genomes]
rs2772390	0.81[ASN][1000 genomes]
rs3117320	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130001	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130002	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130006	0.84[AMR][1000 genomes]
rs3130007	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130015	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130025	0.81[ASN][1000 genomes]
rs3130274	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130275	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130276	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs371005	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs376006	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs391500	0.88[AMR][1000 genomes]
rs420714	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs442745	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs453590	0.81[ASN][1000 genomes]
rs456993	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs459927	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs461887	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4620113	0.85[ASN][1000 genomes]
rs465223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs465474	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs465506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs465877	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs467065	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6942045	0.87[AMR][1000 genomes]
rs7382303	0.82[ASN][1000 genomes]
rs9278025	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9278029	0.86[AMR][1000 genomes]
rs9368760	0.84[AMR][1000 genomes]
rs9380355	0.87[ASN][1000 genomes]
rs9461856	0.80[ASN][1000 genomes]

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	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs461964	LEMD2	cis	parietal	SCAN
rs461964	ETV7	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33358600-33361000	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:33358800-33360800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:33358800-33360800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:33358800-33360800	Active TSS	NHLF	lung
5	chr6:33358800-33361000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:33358800-33361000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:33358800-33361400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:33358800-33361800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:33359000-33360800	Active TSS	Colon Smooth Muscle	Colon
10	chr6:33359000-33361000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:33359000-33361200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr6:33359000-33361200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr6:33359000-33361200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:33359000-33362000	Active TSS	HSMM	muscle
15	chr6:33359000-33362600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:33359200-33360600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:33359200-33360800	Active TSS	GM12878-XiMat	blood
18	chr6:33359200-33361000	Active TSS	Fetal Intestine Large	intestine
19	chr6:33359200-33361200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:33359400-33361200	Enhancers	Spleen	Spleen
21	chr6:33359600-33360600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:33359600-33360600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr6:33359600-33360600	Active TSS	Gastric	stomach
24	chr6:33359600-33360600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr6:33359600-33360800	Active TSS	Muscle Satellite Cultured Cells	--
26	chr6:33359600-33360800	Bivalent/Poised TSS	HepG2	liver
27	chr6:33359600-33360800	Active TSS	NHDF-Ad	bronchial
28	chr6:33359600-33361000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:33359600-33361000	Active TSS	A549	lung
30	chr6:33359600-33361200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr6:33359600-33361200	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr6:33359800-33360600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:33359800-33360600	Flanking Active TSS	Placenta	Placenta
34	chr6:33359800-33360800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr6:33359800-33360800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr6:33359800-33360800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:33359800-33360800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:33359800-33360800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr6:33359800-33360800	Enhancers	Stomach Mucosa	stomach
40	chr6:33359800-33361000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr6:33359800-33361200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:33359800-33361200	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr6:33359800-33363400	Transcr. at gene 5' and 3'	Dnd41	blood
44	chr6:33360000-33360600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:33360000-33360600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:33360000-33360600	Flanking Active TSS	Fetal Brain Female	brain
47	chr6:33360000-33360800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr6:33360000-33360800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:33360000-33360800	Flanking Active TSS	Fetal Lung	lung
50	chr6:33360000-33361000	Flanking Active TSS	Fetal Intestine Small	intestine

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