Variant report

Variant	rs1620976
Chromosome Location	chr5:14830512-14830513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr5:14830301-14830592	MCF10A-Er-Src	breast:	n/a	n/a
2	TAF1	chr5:14830410-14830606	PFSK-1	brain:	n/a	n/a
3	REST	chr5:14830317-14830639	PFSK-1	brain:	n/a	n/a
4	SIN3AK20	chr5:14830413-14830628	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14824343..14826536-chr5:14829301..14831889,2	MCF-7	breast:
2	chr5:14826927..14829271-chr5:14829445..14831346,2	K562	blood:

Variant related genes	Relation type
MIR4637	TF binding region
ENSG00000264792	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1550826	0.85[MKK][hapmap]
rs1679138	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812659	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2448493	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2453320	0.85[ASN][1000 genomes]
rs258220	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs258232	0.85[ASN][1000 genomes]
rs25946	0.84[CHB][hapmap];0.91[MEX][hapmap]
rs26304	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26305	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26306	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27353	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30613	0.94[CHB][hapmap];0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs31907	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs31910	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31911	0.92[CEU][hapmap];0.87[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31917	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31987	0.85[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs31988	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs31989	0.85[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs31990	0.80[CHB][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs379016	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412056	0.83[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs42274	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826351	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826355	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826356	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv948447	chr5:14771247-14852610	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830212	chr5:14784197-14966683	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	esv2753381	chr5:14814900-14882800	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	esv2755533	chr5:14814900-14882800	Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	esv2755538	chr5:14814900-14927500	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1620976	ANKH	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14811600-14843800	Weak transcription	Fetal Intestine Large	intestine
2	chr5:14811600-14861200	Weak transcription	Colonic Mucosa	Colon
3	chr5:14812000-14849600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:14814000-14835000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:14814400-14842200	Weak transcription	Thymus	Thymus
6	chr5:14817400-14842400	Weak transcription	Lung	lung
7	chr5:14818000-14833000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:14819600-14830600	Weak transcription	HSMM	muscle
9	chr5:14819600-14835400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr5:14820000-14830800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr5:14820600-14854800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:14820800-14851800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:14821200-14848600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:14822000-14838000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:14822400-14831200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:14822800-14830600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:14823000-14835200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:14824800-14869600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:14825200-14830800	Weak transcription	Brain Anterior Caudate	brain
20	chr5:14825200-14833000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr5:14825400-14830800	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:14825400-14830800	Weak transcription	Brain Substantia Nigra	brain
23	chr5:14825400-14831200	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:14825600-14831000	Weak transcription	Aorta	Aorta
25	chr5:14826600-14841800	Weak transcription	HepG2	liver
26	chr5:14826800-14830800	Strong transcription	Fetal Intestine Small	intestine
27	chr5:14827000-14831400	Enhancers	Fetal Brain Male	brain
28	chr5:14827200-14832200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr5:14827600-14831600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:14827600-14839000	Weak transcription	Dnd41	blood
31	chr5:14827600-14850000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:14827800-14854600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:14828000-14835000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:14828000-14843800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr5:14828200-14833800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:14828400-14832800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:14828400-14839600	Weak transcription	Primary T cells from cord blood	blood
38	chr5:14828400-14839800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:14828600-14846600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr5:14828800-14856200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr5:14829000-14831800	Enhancers	Psoas Muscle	Psoas
42	chr5:14829600-14832200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr5:14829800-14831200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:14830000-14830800	Enhancers	Liver	Liver
45	chr5:14830000-14831200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:14830000-14831200	Enhancers	HMEC	breast
47	chr5:14830000-14831600	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr5:14830200-14831000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr5:14830200-14831200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:14830200-14831400	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links