Variant report

Variant	rs9348977
Chromosome Location	chr6:35417338-35417339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:226)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:226 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr6:35417178-35417499	GM12878	blood:	n/a	n/a
2	CTCF	chr6:35417280-35417430	NHLF	lung:	n/a	n/a
3	RAD21	chr6:35417142-35417499	GM12878	blood:	n/a	n/a
4	RAD21	chr6:35417148-35417573	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr6:35417260-35417410	HMF	breast:	n/a	n/a
6	RUNX3	chr6:35417235-35417817	GM12878	blood:	n/a	n/a
7	CTCF	chr6:35417280-35417430	HFF	foreskin:	n/a	n/a
8	FOXA1	chr6:35417131-35417594	HepG2	liver:	n/a	n/a
9	CTCF	chr6:35417273-35417499	A549	lung:	n/a	n/a
10	CTCF	chr6:35417258-35417514	GM19238	blood:	n/a	n/a
11	CTCF	chr6:35417280-35417430	HA-sp	spinal cord:	n/a	n/a
12	CTCF	chr6:35417300-35417450	GM12864	blood:	n/a	n/a
13	CTCF	chr6:35417260-35417410	GM12878	blood:	n/a	n/a
14	CTCF	chr6:35417245-35417512	GM12878	blood:	n/a	n/a
15	CTCF	chr6:35417220-35417370	HVMF	connective:	n/a	n/a
16	CTCF	chr6:35417260-35417410	GM12870	blood:	n/a	n/a
17	CTCF	chr6:35417251-35417501	LNCaP	prostate:	n/a	n/a
18	RAD21	chr6:35417004-35417787	ECC-1	luminal epithelium:	n/a	n/a
19	UBTF	chr6:35417237-35417484	K562	blood:	n/a	n/a
20	CTCF	chr6:35417280-35417430	AG09309	skin:	n/a	n/a
21	CTCF	chr6:35417280-35417430	AG09319	gingival:	n/a	n/a
22	CTCF	chr6:35417211-35417527	Spleen_OC	spleen:	n/a	n/a
23	CTCF	chr6:35417143-35417521	A549	lung:	n/a	n/a
24	CTCF	chr6:35417300-35417450	GM12866	blood:	n/a	n/a
25	CTCF	chr6:35417300-35417450	SK-N-SH_RA	brain:	n/a	n/a
26	CTCF	chr6:35417280-35417430	Caco-2	colon:	n/a	n/a
27	EP300	chr6:35417259-35417524	K562	blood:	n/a	n/a
28	CTCF	chr6:35417300-35417450	HPAF	blood vessel:	n/a	n/a
29	MAZ	chr6:35417214-35417544	GM12878	blood:	n/a	n/a
30	CTCF	chr6:35417280-35417430	HCPEpiC	choroid plexus:	n/a	n/a
31	CTCF	chr6:35417260-35417410	GM12801	blood:	n/a	n/a
32	CTCF	chr6:35417215-35417743	HCT-116	colon:	n/a	n/a
33	CTCF	chr6:35417300-35417450	SAEC	small airway:	n/a	n/a
34	CTCF	chr6:35417280-35417430	HPAF	blood vessel:	n/a	n/a
35	CTCF	chr6:35417300-35417450	HL-60	blood:	n/a	n/a
36	SP1	chr6:35417134-35417461	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr6:35417085-35417603	A549	lung:	n/a	n/a
38	CTCF	chr6:35417320-35417470	HRPEpiC	eye:	n/a	n/a
39	CTCF	chr6:35417280-35417430	GM12872	blood:	n/a	n/a
40	CTCF	chr6:35417280-35417430	HUVEC	blood vessel:	n/a	n/a
41	CTCF	chr6:35417179-35417482	SK-N-SH_RA	brain:	n/a	n/a
42	ZNF143	chr6:35417200-35417531	K562	blood:	n/a	n/a
43	CTCF	chr6:35417300-35417450	HCM	heart:	n/a	n/a
44	CTCF	chr6:35417260-35417410	MCF-7	breast:	n/a	n/a
45	CTCF	chr6:35417320-35417470	GM12865	blood:	n/a	n/a
46	CTCF	chr6:35417300-35417450	GM12878	blood:	n/a	n/a
47	ZNF143	chr6:35417181-35417543	GM12878	blood:	n/a	n/a
48	FOXA1	chr6:35417118-35417696	HepG2	liver:	n/a	n/a
49	CTCF	chr6:35417300-35417450	HEK293	kidney:	n/a	n/a
50	CTCF	chr6:35417300-35417450	HA-sp	spinal cord:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35417325..35417921-chr6:35435622..35436536,2	MCF-7	breast:
2	chr6:35415818..35424678-chr6:35432486..35440672,36	K562	blood:
3	chr6:35309690..35310641-chr6:35416899..35417897,7	MCF-7	breast:
4	chr6:35262189..35262830-chr6:35417199..35417947,3	MCF-7	breast:
5	chr6:35309667..35310862-chr6:35416860..35417813,16	K562	blood:
6	chr6:35261989..35262828-chr6:35416846..35417449,3	MCF-7	breast:
7	chr6:35329516..35331357-chr6:35414817..35417634,2	MCF-7	breast:
8	chr6:35264747..35265990-chr6:35416893..35417820,7	MCF-7	breast:
9	chr6:35299795..35300338-chr6:35417088..35417923,2	MCF-7	breast:
10	chr6:35266653..35267496-chr6:35416841..35417464,3	K562	blood:
11	chr6:35387457..35387973-chr6:35417155..35417800,2	MCF-7	breast:
12	chr6:35309295..35311429-chr6:35417090..35418674,2	MCF-7	breast:
13	chr6:35265049..35266094-chr6:35416870..35417859,12	K562	blood:

No data

Variant related genes	Relation type
FANCE	TF binding region
ENSG00000198755	Chromatin interaction
ENSG00000023892	Chromatin interaction
ENSG00000112033	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10947546	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12173925	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3823434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs45551032	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57253134	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73413796	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9368868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv470812	chr6:35374461-35418118	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
5	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
6	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
7	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
8	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35403400-35419400	Weak transcription	Right Atrium	heart
2	chr6:35406800-35419200	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:35411200-35419600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:35411400-35419400	Weak transcription	NHEK	skin
5	chr6:35411600-35419400	Weak transcription	HMEC	breast
6	chr6:35411800-35419200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:35413800-35417400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:35413800-35419400	Weak transcription	Pancreas	Pancrea
9	chr6:35414000-35419200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:35414000-35419200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:35414200-35417400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:35414200-35419000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:35414200-35419000	Weak transcription	Placenta	Placenta
14	chr6:35414200-35419600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:35414400-35417400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:35414400-35419600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:35416200-35418000	Enhancers	Fetal Muscle Trunk	muscle
18	chr6:35416400-35419200	Bivalent Enhancer	HepG2	liver
19	chr6:35416600-35419400	Weak transcription	Brain Substantia Nigra	brain
20	chr6:35417000-35417600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr6:35417000-35417600	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:35417000-35417600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:35417000-35417600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:35417000-35417600	Enhancers	Brain Hippocampus Middle	brain
25	chr6:35417000-35417800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr6:35417000-35417800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:35417000-35417800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr6:35417000-35417800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:35417000-35417800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr6:35417000-35418200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr6:35417200-35417400	Enhancers	Dnd41	blood
32	chr6:35417200-35419200	Weak transcription	Stomach Smooth Muscle	stomach

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