Variant report

Variant	rs6692983
Chromosome Location	chr1:223854684-223854685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:223854076-223854757	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:223854639-223854689	LNCaP	prostate:	n/a
2	chr1:223854639-223854689	HNPCEpiC	eye:	n/a
3	chr1:223854639-223854689	HCPEpiC	choroid plexus:	n/a
4	chr1:223854639-223854689	T-47D	breast:	n/a
5	chr1:223854639-223854689	NT2-D1	testis:	n/a
6	chr1:223854639-223854689	IMR90	lung:	fetal
7	chr1:223854639-223854689	AG10803	skin:	n/a
8	chr1:223854639-223854689	MCF10A-Er-Src	breast:	n/a
9	chr1:223854639-223854689	ovcar-3	ovarian:	n/a
10	chr1:223854639-223854689	AG04450	lung:	fetal
11	chr1:223854639-223854689	PFSK-1	brain:	n/a
12	chr1:223854639-223854689	H1-hESC	embryonic stem cell:	embryo
13	chr1:223854639-223854689	SAEC	small airway:	n/a
14	chr1:223854639-223854689	SKMC	muscle:	n/a
15	chr1:223854639-223854689	CMK	blood:	n/a
16	chr1:223854639-223854689	HepG2	liver:	n/a
17	chr1:223854639-223854689	Jurkat	blood:	n/a
18	chr1:223854639-223854689	NHBE	bronchial:	n/a
19	chr1:223854639-223854689	NB4	blood:	n/a
20	chr1:223854639-223854689	HCM	heart:	n/a
21	chr1:223854639-223854689	NHDF-neo	bronchial:	n/a
22	chr1:223854639-223854689	GM12878	blood:	n/a
23	chr1:223854639-223854689	HPAEpiC	pulmonary alveolar:	n/a
24	chr1:223854639-223854689	AG09319	gingival:	n/a
25	chr1:223854639-223854689	Caco-2	colon:	n/a
26	chr1:223854639-223854689	HCT-116	colon:	n/a
27	chr1:223854639-223854689	HCF	heart:	n/a
28	chr1:223854639-223854689	GM12891	blood:	n/a
29	chr1:223854639-223854689	HRE	kidney:	n/a
30	chr1:223854639-223854689	HL-60	blood:	n/a
31	chr1:223854639-223854689	HRPEpiC	eye:	n/a
32	chr1:223854639-223854689	PrEC	prostate:	n/a
33	chr1:223854639-223854689	HRCEpiC	kidney:	n/a
34	chr1:223854639-223854689	AoSMC	blood vessel:	n/a
35	chr1:223854639-223854689	HIPEpiC	eye:	n/a
36	chr1:223854639-223854689	K562	blood:	n/a
37	chr1:223854639-223854689	HUVEC	blood vessel:	n/a
38	chr1:223854639-223854689	ECC-1	luminal epithelium:	n/a
39	chr1:223854639-223854689	Hepatocyte	liver:	n/a
40	chr1:223854639-223854689	BE2_C	brain:	n/a
41	chr1:223854639-223854689	GM06990	blood:	n/a
42	chr1:223854639-223854689	HEEpiC	esophagus:	n/a
43	chr1:223854639-223854689	SK-N-SH_RA	brain:	n/a
44	chr1:223854639-223854689	MCF-7	breast:	n/a
45	chr1:223854639-223854689	AG09309	skin:	n/a
46	chr1:223854639-223854689	BJ	skin:	n/a
47	chr1:223854639-223854689	AG04449	skin:	fetal
48	chr1:223854639-223854689	GM12892	blood:	n/a
49	chr1:223854639-223854689	NH-A	brain:	n/a
50	chr1:223854639-223854689	HAEpiC	amniotic membrane:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223831956..223833970-chr1:223853050..223855835,2	MCF-7	breast:
2	chr1:223850712..223853354-chr1:223854192..223856571,2	MCF-7	breast:
3	chr1:223836208..223847031-chr1:223849408..223858826,22	MCF-7	breast:
4	chr1:223840282..223843675-chr1:223851675..223856291,7	MCF-7	breast:
5	chr1:223825136..223827090-chr1:223853987..223856973,2	MCF-7	breast:
6	chr1:223348196..223351831-chr1:223853498..223856683,4	MCF-7	breast:
7	chr1:223833055..223835891-chr1:223854048..223855966,2	K562	blood:
8	chr1:223853852..223855706-chr1:223946715..223948642,2	K562	blood:

No data

Variant related genes	Relation type
CAPN8	TF binding region
CAPN8	CpG island
ENSG00000162909	Chromatin interaction
ENSG00000203697	Chromatin interaction
ENSG00000227002	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10799490	0.95[EUR][1000 genomes]
rs10916022	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[ASN][1000 genomes]
rs10916078	0.85[CHB][hapmap]
rs1109221	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1573242	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs1936526	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[EUR][1000 genomes]
rs2000319	0.92[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6676027	0.83[EUR][1000 genomes]
rs6676365	0.88[EUR][1000 genomes]
rs6677519	0.89[EUR][1000 genomes]
rs6680821	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs6699830	0.92[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6704218	0.88[EUR][1000 genomes]
rs7556396	0.90[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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873210	chr1:223707647-223856414	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1000199	chr1:223803545-223854859	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6692983	HLX	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223851800-223857000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:223853000-223855800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:223853400-223855000	Weak transcription	Gastric	stomach
4	chr1:223853400-223856000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:223853400-223856600	Weak transcription	Lung	lung
6	chr1:223853400-223856800	Enhancers	HMEC	breast
7	chr1:223853400-223857000	Enhancers	Stomach Mucosa	stomach
8	chr1:223853800-223854800	Weak transcription	Placenta	Placenta
9	chr1:223853800-223855200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:223853800-223855600	Weak transcription	Pancreas	Pancrea
11	chr1:223853800-223856200	Enhancers	NHEK	skin
12	chr1:223853800-223856600	Weak transcription	Esophagus	oesophagus
13	chr1:223853800-223857000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr1:223853800-223858400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:223854000-223854800	Weak transcription	Colonic Mucosa	Colon
16	chr1:223854000-223855800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:223854200-223855400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:223854600-223855600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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