Variant report

Variant	rs6005868
Chromosome Location	chr22:29165766-29165767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:29165741-29165791	HEK293	kidney:	embryo
2	chr22:29165741-29165791	PFSK-1	brain:	n/a
3	chr22:29165741-29165791	H1-hESC	embryonic stem cell:	embryo
4	chr22:29165741-29165791	MCF10A-Er-Src	breast:	n/a
5	chr22:29165741-29165791	HEEpiC	esophagus:	n/a
6	chr22:29165741-29165791	GM19239	blood:	n/a
7	chr22:29165741-29165791	BE2_C	brain:	n/a
8	chr22:29165741-29165791	HRCEpiC	kidney:	n/a
9	chr22:29165741-29165791	PrEC	prostate:	n/a
10	chr22:29165741-29165791	HepG2	liver:	n/a
11	chr22:29165741-29165791	BJ	skin:	n/a
12	chr22:29165741-29165791	AG04450	lung:	fetal
13	chr22:29165741-29165791	PANC-1	pancreas:	n/a
14	chr22:29165741-29165791	Caco-2	colon:	n/a
15	chr22:29165741-29165791	Jurkat	blood:	n/a
16	chr22:29165741-29165791	SAEC	small airway:	n/a
17	chr22:29165741-29165791	AG04449	skin:	fetal
18	chr22:29165741-29165791	Hepatocyte	liver:	n/a
19	chr22:29165741-29165791	GM12878	blood:	n/a
20	chr22:29165741-29165791	U87	brain:	n/a
21	chr22:29165741-29165791	NH-A	brain:	n/a
22	chr22:29165741-29165791	AG09309	skin:	n/a
23	chr22:29165741-29165791	NHDF-neo	bronchial:	n/a
24	chr22:29165741-29165791	HIPEpiC	eye:	n/a
25	chr22:29165741-29165791	GM06990	blood:	n/a
26	chr22:29165741-29165791	HMEC	breast:	n/a
27	chr22:29165741-29165791	K562	blood:	n/a
28	chr22:29165741-29165791	T-47D	breast:	n/a
29	chr22:29165741-29165791	IMR90	lung:	fetal
30	chr22:29165741-29165791	HCF	heart:	n/a
31	chr22:29165741-29165791	HUVEC	blood vessel:	n/a
32	chr22:29165741-29165791	NT2-D1	testis:	n/a
33	chr22:29165741-29165791	HRE	kidney:	n/a
34	chr22:29165741-29165791	AG09319	gingival:	n/a
35	chr22:29165741-29165791	CMK	blood:	n/a
36	chr22:29165741-29165791	HNPCEpiC	eye:	n/a
37	chr22:29165741-29165791	SK-N-SH_RA	brain:	n/a
38	chr22:29165741-29165791	AG10803	skin:	n/a
39	chr22:29165741-29165791	HPAEpiC	pulmonary alveolar:	n/a
40	chr22:29165741-29165791	ovcar-3	ovarian:	n/a
41	chr22:29165741-29165791	ECC-1	luminal epithelium:	n/a
42	chr22:29165741-29165791	HCT-116	colon:	n/a
43	chr22:29165741-29165791	SK-N-SH	brain:	n/a
44	chr22:29165741-29165791	HCPEpiC	choroid plexus:	n/a
45	chr22:29165741-29165791	LNCaP	prostate:	n/a
46	chr22:29165741-29165791	SKMC	muscle:	n/a
47	chr22:29165741-29165791	GM12891	blood:	n/a
48	chr22:29165741-29165791	HL-60	blood:	n/a
49	chr22:29165741-29165791	NB4	blood:	n/a
50	chr22:29165741-29165791	A549	lung:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr22:29164518..29166292-chr22:29215765..29218524,2	MCF-7	breast:
2	chr22:29163517..29166868-chr22:29167039..29168960,4	K562	blood:
3	chr22:29136893..29139522-chr22:29164321..29165928,2	MCF-7	breast:
4	chr22:29165320..29166855-chr22:29167309..29169712,2	K562	blood:
5	chr22:29134226..29139597-chr22:29164663..29170736,9	K562	blood:

No data

Variant related genes	Relation type
CCDC117	CpG island
ENSG00000183765	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000159873	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12168849	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2206061	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2235432	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294431	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997391	0.81[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs5997393	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997394	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997401	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs6005856	0.84[ASN][1000 genomes]
rs6005857	0.87[ASN][1000 genomes]
rs6005866	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005877	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005899	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs9625562	0.83[EUR][1000 genomes]
rs9625573	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9625575	0.91[JPT][hapmap]

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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29145800-29168000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr22:29148000-29167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:29154400-29167400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:29164400-29166000	Enhancers	HepG2	liver
5	chr22:29164800-29167200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr22:29165400-29165800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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