Variant report

Variant	rs62407572
Chromosome Location	chr6:33561303-33561304
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:183)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr6:33559961-33561426	GM12878	blood:	n/a	n/a
2	ZBTB7A	chr6:33560438-33561443	ECC-1	luminal epithelium:	n/a	n/a
3	ZBTB7A	chr6:33560395-33561493	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr6:33560971-33561433	GM12891	blood:	n/a	n/a
5	PAX5	chr6:33560129-33561311	GM12878	blood:	n/a	chr6:33561019-33561038 chr6:33560403-33560422
6	PML	chr6:33559934-33561467	GM12878	blood:	n/a	n/a
7	STAT5A	chr6:33559941-33561548	GM12878	blood:	n/a	n/a
8	RELA	chr6:33560219-33561454	GM15510	blood:	n/a	n/a
9	POLR2A	chr6:33560932-33561364	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr6:33560447-33561563	ECC-1	luminal epithelium:	n/a	n/a
11	ELF1	chr6:33560137-33561408	GM12878	blood:	n/a	chr6:33561180-33561192
12	ZNF143	chr6:33560837-33561348	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:33560866-33561328	GM12878	blood:	n/a	n/a
14	BCLAF1	chr6:33560764-33561395	GM12878	blood:	n/a	chr6:33561177-33561186
15	PAX5	chr6:33560078-33561324	GM12892	blood:	n/a	chr6:33561019-33561038 chr6:33560403-33560422
16	ZEB1	chr6:33560807-33561313	GM12878	blood:	n/a	n/a
17	PAX5	chr6:33560044-33561443	GM12878	blood:	n/a	chr6:33561019-33561038 chr6:33560403-33560422
18	POLR2A	chr6:33560782-33561500	GM12892	blood:	n/a	n/a
19	POLR2A	chr6:33560862-33561359	GM19193	blood:	n/a	n/a
20	POLR2A	chr6:33560786-33561391	GM12878	blood:	n/a	n/a
21	EP300	chr6:33560598-33561429	ECC-1	luminal epithelium:	n/a	chr6:33561174-33561190
22	TCF12	chr6:33560196-33561521	ECC-1	luminal epithelium:	n/a	n/a
23	RAD21	chr6:33560790-33561343	ECC-1	luminal epithelium:	n/a	n/a
24	RUNX3	chr6:33560001-33561329	GM12878	blood:	n/a	n/a
25	PAX5	chr6:33560719-33561324	GM12878	blood:	n/a	chr6:33561019-33561038
26	TEAD4	chr6:33560348-33561458	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr6:33560742-33561372	GM12892	blood:	n/a	n/a
28	EP300	chr6:33560163-33561554	ECC-1	luminal epithelium:	n/a	chr6:33561174-33561190
29	POLR2A	chr6:33560409-33561372	GM12892	blood:	n/a	n/a
30	TCF12	chr6:33560391-33561581	ECC-1	luminal epithelium:	n/a	n/a
31	MTA3	chr6:33559812-33561588	GM12878	blood:	n/a	n/a
32	CHD2	chr6:33560836-33561330	GM12878	blood:	n/a	n/a
33	MAX	chr6:33560421-33561511	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr6:33560907-33561366	GM18505	blood:	n/a	n/a
35	POLR2A	chr6:33560870-33561453	GM12878	blood:	n/a	n/a
36	TEAD4	chr6:33560827-33561383	ECC-1	luminal epithelium:	n/a	n/a
37	NFIC	chr6:33560471-33561547	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr6:33560869-33561360	GM15510	blood:	n/a	n/a
39	WRNIP1	chr6:33561285-33561444	GM12878	blood:	n/a	n/a
40	MAX	chr6:33560433-33561413	ECC-1	luminal epithelium:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33561266-33561316	SKMC	muscle:	n/a
2	chr6:33561253-33561303	HPAEpiC	pulmonary alveolar:	n/a
3	chr6:33561266-33561316	H1-hESC	embryonic stem cell:	embryo
4	chr6:33561266-33561316	GM12892	blood:	n/a
5	chr6:33561266-33561316	BE2_C	brain:	n/a
6	chr6:33561253-33561303	NH-A	brain:	n/a
7	chr6:33561266-33561316	AG09309	skin:	n/a
8	chr6:33561264-33561314	CMK	blood:	n/a
9	chr6:33561264-33561314	K562	blood:	n/a
10	chr6:33561253-33561303	BE2_C	brain:	n/a
11	chr6:33561266-33561316	HCPEpiC	choroid plexus:	n/a
12	chr6:33561264-33561314	ovcar-3	ovarian:	n/a
13	chr6:33561253-33561303	HNPCEpiC	eye:	n/a
14	chr6:33561264-33561314	GM06990	blood:	n/a
15	chr6:33561264-33561314	U87	brain:	n/a
16	chr6:33561253-33561303	MCF10A-Er-Src	breast:	n/a
17	chr6:33561264-33561314	GM12891	blood:	n/a
18	chr6:33561266-33561316	NT2-D1	testis:	n/a
19	chr6:33561253-33561303	LNCaP	prostate:	n/a
20	chr6:33561264-33561314	Hepatocyte	liver:	n/a
21	chr6:33561266-33561316	HCT-116	colon:	n/a
22	chr6:33561266-33561316	BJ	skin:	n/a
23	chr6:33561253-33561303	HCM	heart:	n/a
24	chr6:33561264-33561314	NB4	blood:	n/a
25	chr6:33561264-33561314	PFSK-1	brain:	n/a
26	chr6:33561264-33561314	GM12878	blood:	n/a
27	chr6:33561266-33561316	GM06990	blood:	n/a
28	chr6:33561253-33561303	Hepatocyte	liver:	n/a
29	chr6:33561253-33561303	ProgFib	skin:	n/a
30	chr6:33561264-33561314	SAEC	small airway:	n/a
31	chr6:33561266-33561316	MCF-7	breast:	n/a
32	chr6:33561264-33561314	H1-hESC	embryonic stem cell:	embryo
33	chr6:33561266-33561316	T-47D	breast:	n/a
34	chr6:33561264-33561314	ECC-1	luminal epithelium:	n/a
35	chr6:33561264-33561314	Caco-2	colon:	n/a
36	chr6:33561266-33561316	NHBE	bronchial:	n/a
37	chr6:33561253-33561303	ECC-1	luminal epithelium:	n/a
38	chr6:33561253-33561303	CMK	blood:	n/a
39	chr6:33561253-33561303	HCPEpiC	choroid plexus:	n/a
40	chr6:33561264-33561314	AG10803	skin:	n/a
41	chr6:33561264-33561314	PANC-1	pancreas:	n/a
42	chr6:33561253-33561303	HCT-116	colon:	n/a
43	chr6:33561266-33561316	HUVEC	blood vessel:	n/a
44	chr6:33561264-33561314	HCT-116	colon:	n/a
45	chr6:33561264-33561314	NT2-D1	testis:	n/a
46	chr6:33561266-33561316	Caco-2	colon:	n/a
47	chr6:33561253-33561303	NHBE	bronchial:	n/a
48	chr6:33561253-33561303	AoSMC	blood vessel:	n/a
49	chr6:33561266-33561316	PFSK-1	brain:	n/a
50	chr6:33561266-33561316	AoSMC	blood vessel:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33555432..33562879-chr6:33670455..33680174,12	K562	blood:

No data

Variant related genes	Relation type
LINC00336	TF binding region
LINC00336	CpG island
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11756691	0.96[ASN][1000 genomes]
rs56717418	0.88[ASN][1000 genomes]
rs57831685	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59600351	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59932271	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61046060	0.88[ASN][1000 genomes]
rs62407594	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62407595	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457734	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6457735	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6457736	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6909440	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6909561	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6929022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7741845	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7745060	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7763103	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7766694	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9469520	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS 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	34 gene(s)	inside rSNPs	diseases
4	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33555800-33561400	Enhancers	Spleen	Spleen
2	chr6:33556600-33561400	Enhancers	Lung	lung
3	chr6:33557000-33561400	Enhancers	HMEC	breast
4	chr6:33558600-33567200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:33559000-33567200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:33559400-33562600	Weak transcription	A549	lung
7	chr6:33559400-33563000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:33559400-33567200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:33559600-33563000	Weak transcription	Hela-S3	cervix
10	chr6:33559600-33569800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:33559800-33562600	Weak transcription	HepG2	liver
12	chr6:33560000-33561400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:33560200-33561600	Flanking Active TSS	GM12878-XiMat	blood
14	chr6:33560200-33561600	Enhancers	NHLF	lung
15	chr6:33560400-33561400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:33560400-33561400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr6:33560400-33561400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr6:33560400-33561400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr6:33560400-33561400	Active TSS	Brain Anterior Caudate	brain
20	chr6:33560400-33561400	Bivalent Enhancer	Fetal Brain Male	brain
21	chr6:33560400-33561400	Enhancers	Gastric	stomach
22	chr6:33560400-33561400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr6:33560400-33561600	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr6:33560400-33561600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr6:33560400-33561600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr6:33560600-33561400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:33560600-33561400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:33560600-33561400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:33560600-33561400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr6:33560600-33561400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:33560600-33561400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:33560600-33561400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:33560600-33561400	Active TSS	Brain Angular Gyrus	brain
34	chr6:33560600-33561400	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr6:33560600-33561400	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr6:33560600-33561400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr6:33560600-33561400	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr6:33560600-33561400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr6:33560600-33561400	Enhancers	NH-A	brain
40	chr6:33560600-33561400	Flanking Active TSS	NHEK	skin
41	chr6:33560600-33561600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr6:33560600-33561600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:33560600-33561600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:33560600-33561600	Enhancers	Pancreas	Pancrea
45	chr6:33560600-33561600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr6:33560800-33561400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:33560800-33561400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:33560800-33561400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr6:33560800-33561400	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr6:33560800-33561400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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