Variant report

Variant	rs6704401
Chromosome Location	chr1:228332081-228332082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr1:228332030-228332338	K562	blood:	n/a	n/a
2	POLR2A	chr1:228331777-228332166	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:228332025-228332528	K562	blood:	n/a	n/a
4	POLR2A	chr1:228327114-228332328	IMR90	lung:	n/a	n/a
5	POLR2A	chr1:228331368-228332307	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:228331544-228333910	K562	blood:	n/a	n/a
7	POLR2A	chr1:228332009-228332563	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:228332058-228332108	AG09319	gingival:	n/a
2	chr1:228332058-228332108	SAEC	small airway:	n/a
3	chr1:228332058-228332108	Jurkat	blood:	n/a
4	chr1:228332058-228332108	BJ	skin:	n/a
5	chr1:228332058-228332108	NB4	blood:	n/a
6	chr1:228332058-228332108	HepG2	liver:	n/a
7	chr1:228332058-228332108	NT2-D1	testis:	n/a
8	chr1:228332058-228332108	HL-60	blood:	n/a
9	chr1:228332058-228332108	NH-A	brain:	n/a
10	chr1:228332058-228332108	IMR90	lung:	fetal
11	chr1:228332058-228332108	HNPCEpiC	eye:	n/a
12	chr1:228332058-228332108	SK-N-SH_RA	brain:	n/a
13	chr1:228332058-228332108	K562	blood:	n/a
14	chr1:228332058-228332108	Hepatocyte	liver:	n/a
15	chr1:228332058-228332108	GM12891	blood:	n/a
16	chr1:228332058-228332108	PFSK-1	brain:	n/a
17	chr1:228332058-228332108	A549	lung:	n/a
18	chr1:228332058-228332108	ECC-1	luminal epithelium:	n/a
19	chr1:228332058-228332108	HIPEpiC	eye:	n/a
20	chr1:228332058-228332108	GM12892	blood:	n/a
21	chr1:228332058-228332108	ovcar-3	ovarian:	n/a
22	chr1:228332058-228332108	HRPEpiC	eye:	n/a
23	chr1:228332058-228332108	AG04450	lung:	fetal
24	chr1:228332058-228332108	Caco-2	colon:	n/a
25	chr1:228332058-228332108	PrEC	prostate:	n/a
26	chr1:228332058-228332108	AG09309	skin:	n/a
27	chr1:228332058-228332108	AG10803	skin:	n/a
28	chr1:228332058-228332108	AG04449	skin:	fetal
29	chr1:228332058-228332108	SKMC	muscle:	n/a
30	chr1:228332058-228332108	T-47D	breast:	n/a
31	chr1:228332058-228332108	LNCaP	prostate:	n/a
32	chr1:228332058-228332108	NHDF-neo	bronchial:	n/a
33	chr1:228332058-228332108	HRE	kidney:	n/a
34	chr1:228332058-228332108	GM12878	blood:	n/a
35	chr1:228332058-228332108	H1-hESC	embryonic stem cell:	embryo
36	chr1:228332058-228332108	HEK293	kidney:	embryo
37	chr1:228332058-228332108	HCT-116	colon:	n/a
38	chr1:228332058-228332108	MCF10A-Er-Src	breast:	n/a
39	chr1:228332058-228332108	HUVEC	blood vessel:	n/a
40	chr1:228332058-228332108	PANC-1	pancreas:	n/a
41	chr1:228332058-228332108	RPTEC	kidney:	n/a
42	chr1:228332058-228332108	SK-N-SH	brain:	n/a
43	chr1:228332058-228332108	HEEpiC	esophagus:	n/a
44	chr1:228332058-228332108	MCF-7	breast:	n/a
45	chr1:228332058-228332108	U87	brain:	n/a
46	chr1:228332058-228332108	BE2_C	brain:	n/a
47	chr1:228332058-228332108	HAEpiC	amniotic membrane:	n/a
48	chr1:228332058-228332108	HCF	heart:	n/a
49	chr1:228332058-228332108	AoSMC	blood vessel:	n/a
50	chr1:228332058-228332108	HRCEpiC	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr1:228331165..228333412-chr1:228361433..228363518,2	MCF-7	breast:
2	chr1:228284520..228292111-chr1:228324853..228335412,14	K562	blood:
3	chr1:228295402..228297803-chr1:228330568..228332279,2	MCF-7	breast:

No data

Variant related genes	Relation type
GUK1	TF binding region
GUK1	CpG island
ENSG00000162910	Chromatin interaction
ENSG00000264944	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000181873	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs2231715	1.00[AMR][1000 genomes]
rs2231720	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56756911	1.00[AMR][1000 genomes]
rs56832724	1.00[AMR][1000 genomes]
rs56921575	0.86[AFR][1000 genomes]
rs56986798	1.00[AMR][1000 genomes]
rs57053910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59699324	1.00[AMR][1000 genomes]
rs61413658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6694537	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092912	1.00[AMR][1000 genomes]
rs73092923	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092944	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092953	1.00[AMR][1000 genomes]
rs73092954	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092957	1.00[AMR][1000 genomes]
rs73092959	1.00[AMR][1000 genomes]
rs73092999	1.00[AMR][1000 genomes]
rs73095404	1.00[AMR][1000 genomes]
rs73095424	1.00[AMR][1000 genomes]
rs73095429	1.00[AMR][1000 genomes]
rs73095437	1.00[AMR][1000 genomes]
rs73095449	1.00[AMR][1000 genomes]
rs73097306	0.87[AFR][1000 genomes]
rs73097318	0.87[AFR][1000 genomes]
rs73110726	0.86[AFR][1000 genomes]
rs73110739	0.86[AFR][1000 genomes]
rs73110775	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
5	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
9	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised 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 miRNA target site	106 gene(s)	inside rSNPs	diseases
10	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
11	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
12	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
13	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228329000-228332200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:228329000-228336800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:228329000-228339400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:228329000-228339600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:228329200-228332600	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:228329200-228337400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:228329400-228333200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:228329400-228333800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:228329400-228333800	Genic enhancers	Spleen	Spleen
10	chr1:228329400-228336600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:228329400-228337600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:228329400-228337600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:228329400-228338200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:228329600-228332800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:228329600-228335200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:228329600-228335600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:228329600-228336800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:228329800-228332200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:228329800-228332200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr1:228329800-228332600	Enhancers	Brain Anterior Caudate	brain
21	chr1:228329800-228332800	Enhancers	Liver	Liver
22	chr1:228329800-228336400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:228329800-228336600	Weak transcription	A549	lung
24	chr1:228330000-228332200	Enhancers	Right Atrium	heart
25	chr1:228330000-228332600	Enhancers	Primary T cells from cord blood	blood
26	chr1:228330000-228332600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr1:228330000-228332600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:228330000-228332600	Enhancers	Left Ventricle	heart
29	chr1:228330000-228332600	Enhancers	Stomach Mucosa	stomach
30	chr1:228330000-228332800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:228330000-228333200	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr1:228330000-228333600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:228330000-228334800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:228330000-228335800	Weak transcription	Fetal Lung	lung
35	chr1:228330000-228337200	Genic enhancers	Fetal Muscle Leg	muscle
36	chr1:228330000-228337800	Genic enhancers	Lung	lung
37	chr1:228330200-228332200	Enhancers	Colonic Mucosa	Colon
38	chr1:228330200-228333200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:228330200-228333200	Genic enhancers	Gastric	stomach
40	chr1:228330200-228333200	Enhancers	Right Ventricle	heart
41	chr1:228330200-228333400	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr1:228330200-228333600	Weak transcription	Ovary	ovary
43	chr1:228330200-228336200	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:228330400-228332200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:228330400-228332200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:228330400-228332200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:228330400-228332400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:228330400-228332400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr1:228330400-228332400	Enhancers	Brain Hippocampus Middle	brain
50	chr1:228330400-228332400	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links