Variant report

Variant	rs2307387
Chromosome Location	chr6:88299805-88299806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:477)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:477 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ETS1	chr6:88299479-88300139	A549	lung:	n/a	chr6:88299750-88299763
2	TAF1	chr6:88299458-88300117	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:88299438-88300131	GM18951	blood:	n/a	n/a
4	RELA	chr6:88299475-88300090	GM10847	blood:	n/a	chr6:88299844-88299853 chr6:88299844-88299853
5	RUNX3	chr6:88299386-88300272	GM12878	blood:	n/a	n/a
6	RUNX3	chr6:88299337-88300299	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:88299327-88300184	PANC-1	pancreas:	n/a	n/a
8	MAX	chr6:88299442-88300084	K562	blood:	n/a	n/a
9	PBX3	chr6:88299403-88300146	SK-N-SH	brain:	n/a	chr6:88299782-88299791
10	POLR2A	chr6:88299252-88300238	GM12892	blood:	n/a	n/a
11	RFX5	chr6:88299633-88300112	GM12878	blood:	n/a	chr6:88299782-88299791
12	ZNF143	chr6:88299487-88300318	H1-hESC	embryonic stem cell:	n/a	n/a
13	GABPA	chr6:88299060-88300322	A549	lung:	n/a	n/a
14	RAD21	chr6:88299445-88300064	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:88299510-88300138	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:88299491-88300073	A549	lung:	n/a	n/a
17	POLR2A	chr6:88299432-88300185	GM12891	blood:	n/a	n/a
18	ELF1	chr6:88299396-88300250	MCF-7	breast:	n/a	n/a
19	PAX5	chr6:88299511-88300262	GM12878	blood:	n/a	chr6:88299831-88299840
20	SIN3AK20	chr6:88299440-88299986	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr6:88299330-88300255	NB4	blood:	n/a	n/a
22	POLR2A	chr6:88299262-88300228	HUVEC	blood vessel:	n/a	n/a
23	SRF	chr6:88299552-88299825	K562	blood:	n/a	n/a
24	TAF1	chr6:88299509-88300032	PFSK-1	brain:	n/a	n/a
25	BHLHE40	chr6:88299176-88300272	K562	blood:	n/a	chr6:88299823-88299839
26	ELF1	chr6:88299322-88300166	GM12878	blood:	n/a	n/a
27	TAF1	chr6:88299403-88300143	HepG2	liver:	n/a	n/a
28	POLR2A	chr6:88298921-88300389	HepG2	liver:	n/a	n/a
29	ETS1	chr6:88299535-88299977	K562	blood:	n/a	chr6:88299750-88299763
30	MAX	chr6:88299453-88300117	K562	blood:	n/a	n/a
31	CTCF	chr6:88299780-88299930	HUVEC	blood vessel:	n/a	n/a
32	CEBPD	chr6:88299429-88300125	K562	blood:	n/a	n/a
33	NFIC	chr6:88299453-88300114	HepG2	liver:	n/a	n/a
34	REST	chr6:88299332-88300054	HepG2	liver:	n/a	n/a
35	SP1	chr6:88299222-88300222	HCT-116	colon:	n/a	chr6:88299780-88299801
36	MYC	chr6:88299567-88299999	H1-hESC	embryonic stem cell:	n/a	n/a
37	KAP1	chr6:88299552-88300090	U2OS	brain:	n/a	n/a
38	EBF1	chr6:88299601-88299913	GM12878	blood:	n/a	n/a
39	PML	chr6:88299360-88300242	K562	blood:	n/a	n/a
40	SMC3	chr6:88299471-88300243	Hela-S3	cervix:	n/a	n/a
41	USF2	chr6:88299556-88300267	H1-hESC	embryonic stem cell:	n/a	chr6:88299823-88299839
42	SPI1	chr6:88299404-88300138	HL-60	blood:	n/a	chr6:88299499-88299512
43	RCOR1	chr6:88299195-88300503	HepG2	liver:	n/a	n/a
44	GABPA	chr6:88299437-88300013	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr6:88299425-88300103	GM15510	blood:	n/a	n/a
46	GTF2F1	chr6:88299548-88300163	K562	blood:	n/a	n/a
47	POLR2A	chr6:88299333-88300350	HL-60	blood:	n/a	n/a
48	SP1	chr6:88299497-88300076	GM12878	blood:	n/a	chr6:88299780-88299801
49	POLR2A	chr6:88299102-88300725	HepG2	liver:	n/a	n/a
50	GABPA	chr6:88299431-88300049	HL-60	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:88298942..88303064-chr6:88409165..88412231,4	K562	blood:
2	chr6:88299129..88299891-chr8:92081843..92082472,2	NB4	blood:
3	chr15:100105492..100106141-chr6:88299353..88300156,2	NB4	blood:
4	chr6:88299673..88301546-chr6:89673147..89674942,2	K562	blood:
5	chr1:117602497..117603240-chr6:88299651..88300387,2	Hela-S3	cervix:
6	chr6:88299553..88301559-chr6:88410382..88412634,2	MCF-7	breast:
7	chr20:18547409..18548100-chr6:88299330..88300266,2	NB4	blood:
8	chr6:88299642..88300403-chrX:47076850..47077430,2	Hela-S3	cervix:
9	chr6:88181710..88183852-chr6:88298759..88301128,2	K562	blood:
10	chr6:88299715..88302499-chr6:88315597..88317409,2	MCF-7	breast:
11	chr6:88277452..88280023-chr6:88298199..88301235,3	MCF-7	breast:

No data

Variant related genes	Relation type
RARS2	TF binding region
ORC3	TF binding region
ENSG00000146282	Chromatin interaction
ENSG00000164414	Chromatin interaction
ENSG00000116830	Chromatin interaction
ENSG00000203863	Chromatin interaction
ENSG00000111880	Chromatin interaction
ENSG00000232388	Chromatin interaction
ENSG00000135336	Chromatin interaction
ENSG00000102225	Chromatin interaction
ENSG00000068305	Chromatin interaction
ENSG00000135334	Chromatin interaction
ENSG00000253738	Chromatin interaction
ENSG00000155100	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13193911	0.88[AFR][1000 genomes]
rs13203790	0.92[AFR][1000 genomes]
rs28381452	0.85[AFR][1000 genomes]
rs28385632	0.92[AFR][1000 genomes]
rs34385811	0.92[AFR][1000 genomes]
rs4132445	0.85[AFR][1000 genomes]
rs57804146	1.00[AMR][1000 genomes]
rs62417699	0.92[AFR][1000 genomes]
rs62417701	0.83[AFR][1000 genomes]
rs6902069	0.92[AFR][1000 genomes]
rs6902249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6907499	1.00[AMR][1000 genomes]
rs6911680	1.00[AMR][1000 genomes]
rs6927654	0.92[AFR][1000 genomes]
rs6927826	0.92[AFR][1000 genomes]
rs6929542	0.92[AFR][1000 genomes]
rs6940675	0.85[AFR][1000 genomes]
rs7738268	0.80[AFR][1000 genomes]
rs7759648	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88297800-88301200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:88297800-88301400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:88298000-88300600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:88298000-88300800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:88298000-88301000	Active TSS	HSMM	muscle
6	chr6:88298000-88301400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:88298000-88301400	Active TSS	A549	lung
8	chr6:88298200-88300600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:88298200-88300600	Active TSS	Colonic Mucosa	Colon
10	chr6:88298200-88300800	Active TSS	Fetal Intestine Large	intestine
11	chr6:88298200-88301000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:88298200-88301000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:88298200-88301200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:88298400-88300200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr6:88298400-88300400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:88298400-88300600	Active TSS	Fetal Stomach	stomach
17	chr6:88298400-88300600	Active TSS	Lung	lung
18	chr6:88298400-88300800	Active TSS	Fetal Muscle Trunk	muscle
19	chr6:88298400-88300800	Active TSS	Right Atrium	heart
20	chr6:88298400-88300800	Active TSS	HSMMtube	muscle
21	chr6:88298400-88301000	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr6:88298600-88300600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:88298600-88300600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:88298600-88300600	Active TSS	Ovary	ovary
25	chr6:88298600-88300600	Active TSS	Pancreas	Pancrea
26	chr6:88298600-88300600	Active TSS	HMEC	breast
27	chr6:88298600-88300600	Active TSS	K562	blood
28	chr6:88298600-88300600	Active TSS	NHLF	lung
29	chr6:88298600-88300800	Active TSS	Aorta	Aorta
30	chr6:88298600-88300800	Active TSS	Left Ventricle	heart
31	chr6:88298600-88300800	Active TSS	Psoas Muscle	Psoas
32	chr6:88298600-88301000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr6:88298600-88301000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:88298800-88300200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:88298800-88300400	Active TSS	Muscle Satellite Cultured Cells	--
36	chr6:88298800-88300400	Active TSS	Brain Anterior Caudate	brain
37	chr6:88298800-88300400	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr6:88298800-88300400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr6:88298800-88300400	Active TSS	Fetal Lung	lung
40	chr6:88298800-88300400	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr6:88298800-88300400	Active TSS	Stomach Mucosa	stomach
42	chr6:88298800-88300400	Active TSS	HUVEC	blood vessel
43	chr6:88298800-88300400	Active TSS	NH-A	brain
44	chr6:88298800-88300400	Active TSS	Osteobl	bone
45	chr6:88298800-88300600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:88298800-88300600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:88298800-88300600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:88298800-88300600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:88298800-88300600	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr6:88298800-88300600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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