Variant report

Variant	rs6935954
Chromosome Location	chr6:26255451-26255452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:26255426-26255699	NB4	blood:	n/a	n/a
2	POLR2A	chr6:26254742-26256742	K562	blood:	n/a	n/a
3	TAF7	chr6:26255384-26255631	K562	blood:	n/a	n/a
4	POLR2A	chr6:26254817-26255751	K562	blood:	n/a	n/a
5	POLR2A	chr6:26254802-26255713	MCF-7	breast:	n/a	n/a
6	POLR2A	chr6:26254986-26255452	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:26255016-26255660	H1-hESC	embryonic stem cell:	n/a	n/a
8	HEY1	chr6:26255284-26255752	K562	blood:	n/a	n/a
9	POLR2A	chr6:26254754-26255642	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:26255439-26255489	SAEC	small airway:	n/a
2	chr6:26255439-26255489	HIPEpiC	eye:	n/a
3	chr6:26255439-26255489	HCT-116	colon:	n/a
4	chr6:26255439-26255489	BJ	skin:	n/a
5	chr6:26255439-26255489	PrEC	prostate:	n/a
6	chr6:26255439-26255489	MCF-7	breast:	n/a
7	chr6:26255439-26255489	SK-N-SH	brain:	n/a
8	chr6:26255439-26255489	HRPEpiC	eye:	n/a
9	chr6:26255439-26255489	HAEpiC	amniotic membrane:	n/a
10	chr6:26255439-26255489	Hela-S3	cervix:	n/a
11	chr6:26255439-26255489	HepG2	liver:	n/a
12	chr6:26255439-26255489	GM12891	blood:	n/a
13	chr6:26255439-26255489	AG04450	lung:	fetal
14	chr6:26255439-26255489	HRE	kidney:	n/a
15	chr6:26255439-26255489	A549	lung:	n/a
16	chr6:26255439-26255489	HCPEpiC	choroid plexus:	n/a
17	chr6:26255439-26255489	AG09309	skin:	n/a
18	chr6:26255439-26255489	HUVEC	blood vessel:	n/a
19	chr6:26255439-26255489	ECC-1	luminal epithelium:	n/a
20	chr6:26255439-26255489	U87	brain:	n/a
21	chr6:26255439-26255489	HPAEpiC	pulmonary alveolar:	n/a
22	chr6:26255439-26255489	SK-N-MC	brain:	n/a
23	chr6:26255439-26255489	SK-N-SH_RA	brain:	n/a
24	chr6:26255439-26255489	PANC-1	pancreas:	n/a
25	chr6:26255439-26255489	ProgFib	skin:	n/a
26	chr6:26255439-26255489	LNCaP	prostate:	n/a
27	chr6:26255439-26255489	NHDF-neo	bronchial:	n/a
28	chr6:26255439-26255489	HEEpiC	esophagus:	n/a
29	chr6:26255439-26255489	Jurkat	blood:	n/a
30	chr6:26255439-26255489	AG09319	gingival:	n/a
31	chr6:26255439-26255489	NH-A	brain:	n/a
32	chr6:26255439-26255489	IMR90	lung:	fetal
33	chr6:26255439-26255489	HNPCEpiC	eye:	n/a
34	chr6:26255439-26255489	T-47D	breast:	n/a
35	chr6:26255439-26255489	Hepatocyte	liver:	n/a
36	chr6:26255439-26255489	HMEC	breast:	n/a
37	chr6:26255439-26255489	SKMC	muscle:	n/a
38	chr6:26255439-26255489	K562	blood:	n/a
39	chr6:26255439-26255489	NHBE	bronchial:	n/a
40	chr6:26255439-26255489	GM06990	blood:	n/a
41	chr6:26255439-26255489	CMK	blood:	n/a
42	chr6:26255439-26255489	BE2_C	brain:	n/a
43	chr6:26255439-26255489	H1-hESC	embryonic stem cell:	embryo
44	chr6:26255439-26255489	Caco-2	colon:	n/a
45	chr6:26255439-26255489	HCF	heart:	n/a
46	chr6:26255439-26255489	HL-60	blood:	n/a
47	chr6:26255439-26255489	PFSK-1	brain:	n/a
48	chr6:26255439-26255489	MCF10A-Er-Src	breast:	n/a
49	chr6:26255439-26255489	GM19239	blood:	n/a
50	chr6:26255439-26255489	NB4	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26254262..26255882-chr6:26519341..26520974,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H3F	TF binding region
HIST1H3F	CpG island
ENSG00000199289	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1543681	0.88[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs2179152	0.86[MEX][hapmap]
rs2393592	0.82[GIH][hapmap]
rs2393593	0.80[MEX][hapmap]
rs3999544	0.82[GIH][hapmap]
rs4145878	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs806785	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs806789	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs806795	0.88[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs806977	0.88[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs809871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393692	0.82[GIH][hapmap]
rs9467703	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
8	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
9	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
10	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
11	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
12	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
13	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
14	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
15	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases
16	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6935954	ZSCAN23	cis	cerebellum	SCAN
rs6935954	ZNF187	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26252400-26271200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:26253200-26255600	Weak transcription	Small Intestine	intestine
3	chr6:26253800-26255800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr6:26253800-26257000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:26253800-26257200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:26253800-26257400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:26253800-26257400	Weak transcription	Right Atrium	heart
8	chr6:26253800-26258400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:26253800-26260600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:26253800-26265400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:26253800-26271000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:26254000-26255600	Enhancers	Primary B cells from cord blood	blood
13	chr6:26254000-26257400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:26254000-26257600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:26254000-26259800	Weak transcription	Fetal Kidney	kidney
16	chr6:26254000-26261800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:26254200-26255600	Enhancers	Primary T cells from cord blood	blood
18	chr6:26254200-26257200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:26254200-26257400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:26254200-26257400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:26254200-26257400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:26254200-26257400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:26254200-26258200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:26254200-26258400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:26254200-26258400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:26254200-26258400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:26254200-26258800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:26254200-26269200	Weak transcription	Fetal Stomach	stomach
29	chr6:26254600-26255800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr6:26254600-26258400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr6:26254600-26260000	Weak transcription	Placenta	Placenta
32	chr6:26254800-26255600	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr6:26255000-26255600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr6:26255000-26255600	Flanking Active TSS	GM12878-XiMat	blood
35	chr6:26255000-26255800	Enhancers	Fetal Muscle Leg	muscle
36	chr6:26255000-26269400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:26255200-26255600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:26255200-26255600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:26255200-26256200	Genic enhancers	K562	blood
40	chr6:26255200-26257400	Weak transcription	Brain Germinal Matrix	brain
41	chr6:26255400-26255600	Enhancers	Dnd41	blood
42	chr6:26255400-26255800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:26255400-26256000	Enhancers	HepG2	liver
44	chr6:26255400-26256200	Genic enhancers	Fetal Thymus	thymus
45	chr6:26255400-26256200	Genic enhancers	Thymus	Thymus
46	chr6:26255400-26256600	Genic enhancers	Fetal Intestine Small	intestine
47	chr6:26255400-26257000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr6:26255400-26257200	Enhancers	Fetal Intestine Large	intestine
49	chr6:26255400-26257200	Weak transcription	Stomach Mucosa	stomach
50	chr6:26255400-26257400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links