Variant report

Variant	rs12215920
Chromosome Location	chr6:35474073-35474074
allele	C/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:0)
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	HMGN3	chr6:35474039-35474121	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:35474064-35474114	K562	blood:	n/a
2	chr6:35474064-35474114	AG10803	skin:	n/a
3	chr6:35474064-35474114	NHBE	bronchial:	n/a
4	chr6:35474064-35474114	NH-A	brain:	n/a
5	chr6:35474064-35474114	GM12878	blood:	n/a
6	chr6:35474064-35474114	PANC-1	pancreas:	n/a
7	chr6:35474064-35474114	Caco-2	colon:	n/a
8	chr6:35474064-35474114	SK-N-SH	brain:	n/a
9	chr6:35474064-35474114	SK-N-MC	brain:	n/a
10	chr6:35474064-35474114	GM12892	blood:	n/a
11	chr6:35474064-35474114	ECC-1	luminal epithelium:	n/a
12	chr6:35474064-35474114	CMK	blood:	n/a
13	chr6:35474064-35474114	ProgFib	skin:	n/a
14	chr6:35474064-35474114	RPTEC	kidney:	n/a
15	chr6:35474064-35474114	Hela-S3	cervix:	n/a
16	chr6:35474064-35474114	NB4	blood:	n/a
17	chr6:35474064-35474114	Jurkat	blood:	n/a
18	chr6:35474064-35474114	GM06990	blood:	n/a
19	chr6:35474064-35474114	SKMC	muscle:	n/a
20	chr6:35474064-35474114	PrEC	prostate:	n/a
21	chr6:35474064-35474114	MCF10A-Er-Src	breast:	n/a
22	chr6:35474064-35474114	BE2_C	brain:	n/a
23	chr6:35474064-35474114	HL-60	blood:	n/a
24	chr6:35474064-35474114	HRE	kidney:	n/a
25	chr6:35474064-35474114	HCT-116	colon:	n/a
26	chr6:35474064-35474114	HCPEpiC	choroid plexus:	n/a
27	chr6:35474064-35474114	BJ	skin:	n/a
28	chr6:35474064-35474114	AoSMC	blood vessel:	n/a
29	chr6:35474064-35474114	HNPCEpiC	eye:	n/a
30	chr6:35474064-35474114	HRCEpiC	kidney:	n/a
31	chr6:35474064-35474114	MCF-7	breast:	n/a
32	chr6:35474064-35474114	HepG2	liver:	n/a
33	chr6:35474064-35474114	HEK293	kidney:	embryo
34	chr6:35474064-35474114	U87	brain:	n/a
35	chr6:35474064-35474114	SAEC	small airway:	n/a
36	chr6:35474064-35474114	HCM	heart:	n/a
37	chr6:35474064-35474114	PFSK-1	brain:	n/a
38	chr6:35474064-35474114	HCF	heart:	n/a
39	chr6:35474064-35474114	HIPEpiC	eye:	n/a
40	chr6:35474064-35474114	T-47D	breast:	n/a
41	chr6:35474064-35474114	IMR90	lung:	fetal
42	chr6:35474064-35474114	GM12891	blood:	n/a
43	chr6:35474064-35474114	SK-N-SH_RA	brain:	n/a
44	chr6:35474064-35474114	GM19239	blood:	n/a
45	chr6:35474064-35474114	AG04450	lung:	fetal
46	chr6:35474064-35474114	HUVEC	blood vessel:	n/a
47	chr6:35474064-35474114	HAEpiC	amniotic membrane:	n/a
48	chr6:35474064-35474114	ovcar-3	ovarian:	n/a
49	chr6:35474064-35474114	AG04449	skin:	fetal
50	chr6:35474064-35474114	HEEpiC	esophagus:	n/a

No data

Variant related genes	Relation type
TULP1	TF binding region
TULP1	CpG island

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12181820	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12210757	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2064317	0.93[JPT][hapmap]
rs2395628	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744287	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470043	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv984463	chr6:35432948-35477634	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	67 gene(s)	inside rSNPs	diseases
3	nsv462909	chr6:35457396-35502202	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	nsv602912	chr6:35457396-35502202	Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
5	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	esv2761067	chr6:35471246-35573245	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 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	chr6:35466400-35476800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:35466400-35479200	Weak transcription	Right Ventricle	heart
3	chr6:35466800-35477000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:35466800-35479400	Weak transcription	Right Atrium	heart
5	chr6:35467400-35478600	Weak transcription	Fetal Lung	lung
6	chr6:35469200-35474200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:35473200-35474200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr6:35473200-35474200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr6:35473200-35474400	Flanking Bivalent TSS/Enh	HepG2	liver
10	chr6:35473400-35479400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:35473600-35474200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
12	chr6:35473600-35474200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:35473600-35474200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr6:35473600-35474200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:35473600-35474200	Enhancers	HMEC	breast
16	chr6:35473600-35474400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr6:35473600-35474600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:35473600-35474800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
19	chr6:35473600-35477000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:35473800-35474200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:35473800-35474200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:35473800-35474200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:35473800-35474200	Bivalent Enhancer	Ovary	ovary
24	chr6:35473800-35474600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:35473800-35475400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:35474000-35474200	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr6:35474000-35474200	Bivalent Enhancer	Fetal Stomach	stomach
28	chr6:35474000-35474400	Bivalent Enhancer	Fetal Intestine Large	intestine
29	chr6:35474000-35476000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:35474000-35476800	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links