Variant report

Variant	rs6455360
Chromosome Location	chr6:70990383-70990384
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:70990160-70990626	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr6:70990039-70990660	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr6:70990043-70990463	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr6:70990110-70990403	H1-hESC	embryonic stem cell:	n/a	n/a
5	TEAD4	chr6:70989902-70990462	H1-hESC	embryonic stem cell:	n/a	chr6:70990018-70990027

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:70990361-70990411	T-47D	breast:	n/a
2	chr6:70990361-70990411	HRPEpiC	eye:	n/a
3	chr6:70990361-70990411	GM12891	blood:	n/a
4	chr6:70990361-70990411	HCM	heart:	n/a
5	chr6:70990361-70990411	HIPEpiC	eye:	n/a
6	chr6:70990361-70990411	SK-N-SH	brain:	n/a
7	chr6:70990361-70990411	AoSMC	blood vessel:	n/a
8	chr6:70990361-70990411	A549	lung:	n/a
9	chr6:70990361-70990411	HPAEpiC	pulmonary alveolar:	n/a
10	chr6:70990361-70990411	H1-hESC	embryonic stem cell:	embryo
11	chr6:70990361-70990411	GM19239	blood:	n/a
12	chr6:70990361-70990411	HepG2	liver:	n/a
13	chr6:70990361-70990411	HNPCEpiC	eye:	n/a
14	chr6:70990361-70990411	PFSK-1	brain:	n/a
15	chr6:70990361-70990411	ovcar-3	ovarian:	n/a
16	chr6:70990361-70990411	MCF10A-Er-Src	breast:	n/a
17	chr6:70990361-70990411	Hepatocyte	liver:	n/a
18	chr6:70990361-70990411	ECC-1	luminal epithelium:	n/a
19	chr6:70990361-70990411	AG04450	lung:	fetal
20	chr6:70990361-70990411	PrEC	prostate:	n/a
21	chr6:70990361-70990411	AG04449	skin:	fetal
22	chr6:70990361-70990411	SK-N-SH_RA	brain:	n/a
23	chr6:70990361-70990411	HMEC	breast:	n/a
24	chr6:70990361-70990411	AG09319	gingival:	n/a
25	chr6:70990361-70990411	CMK	blood:	n/a
26	chr6:70990361-70990411	MCF-7	breast:	n/a
27	chr6:70990361-70990411	AG10803	skin:	n/a
28	chr6:70990361-70990411	Caco-2	colon:	n/a
29	chr6:70990361-70990411	Jurkat	blood:	n/a
30	chr6:70990361-70990411	ProgFib	skin:	n/a
31	chr6:70990361-70990411	NB4	blood:	n/a
32	chr6:70990361-70990411	AG09309	skin:	n/a
33	chr6:70990361-70990411	NT2-D1	testis:	n/a
34	chr6:70990361-70990411	SKMC	muscle:	n/a
35	chr6:70990361-70990411	GM12892	blood:	n/a
36	chr6:70990361-70990411	K562	blood:	n/a
37	chr6:70990361-70990411	BJ	skin:	n/a
38	chr6:70990361-70990411	HRCEpiC	kidney:	n/a
39	chr6:70990361-70990411	SK-N-MC	brain:	n/a
40	chr6:70990361-70990411	HCF	heart:	n/a
41	chr6:70990361-70990411	HAEpiC	amniotic membrane:	n/a
42	chr6:70990361-70990411	GM06990	blood:	n/a
43	chr6:70990361-70990411	HCPEpiC	choroid plexus:	n/a
44	chr6:70990361-70990411	Hela-S3	cervix:	n/a
45	chr6:70990361-70990411	U87	brain:	n/a
46	chr6:70990361-70990411	LNCaP	prostate:	n/a
47	chr6:70990361-70990411	HCT-116	colon:	n/a
48	chr6:70990361-70990411	HEK293	kidney:	embryo
49	chr6:70990361-70990411	SAEC	small airway:	n/a
50	chr6:70990361-70990411	GM12878	blood:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:70969310..70971265-chr6:70989015..70991528,2	K562	blood:
2	chr6:70930597..70933117-chr6:70988758..70990429,2	K562	blood:
3	chr6:70983202..70984971-chr6:70988155..70990490,2	K562	blood:

No data

Variant related genes	Relation type
COL9A1	TF binding region
COL9A1	CpG island
ENSG00000112280	Chromatin interaction
ENSG00000253809	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs3806095	0.82[AFR][1000 genomes]
rs7764042	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs7764822	0.84[CEU][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][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	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS 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	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70965200-70991600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:70979000-70991600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:70981400-70991200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:70984200-70992000	Weak transcription	Gastric	stomach
5	chr6:70987600-70991600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:70987600-70992000	Weak transcription	Right Atrium	heart
7	chr6:70989800-70990600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:70990000-70990400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr6:70990000-70990400	Enhancers	H9 Cell Line	embryonic stem cell
10	chr6:70990000-70990400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:70990000-70990400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
12	chr6:70990000-70990600	Enhancers	Esophagus	oesophagus
13	chr6:70990000-70990600	Enhancers	Fetal Brain Female	brain
14	chr6:70990000-70990800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:70990000-70991600	Enhancers	K562	blood
16	chr6:70990000-70992800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr6:70990000-70993400	Enhancers	Fetal Brain Male	brain
18	chr6:70990200-70990400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr6:70990200-70990400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
20	chr6:70990200-70990400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
21	chr6:70990200-70990400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
22	chr6:70990200-70990400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:70990200-70990400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:70990200-70990400	Enhancers	Lung	lung
25	chr6:70990200-70990600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr6:70990200-70990600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
27	chr6:70990200-70990600	Enhancers	Pancreas	Pancrea
28	chr6:70990200-70990800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:70990200-70991600	Enhancers	Brain Germinal Matrix	brain
30	chr6:70990200-70991600	Bivalent Enhancer	Fetal Stomach	stomach

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