Variant report

Variant	rs776594
Chromosome Location	chr4:48638206-48638207
allele	C/T
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	FOXA1	chr4:48637921-48638350	HepG2	liver:	n/a	chr4:48638193-48638208
2	FOXA1	chr4:48637950-48638291	A549	lung:	n/a	chr4:48638193-48638208
3	NR3C1	chr4:48637970-48638302	A549	lung:	n/a	chr4:48638160-48638176 chr4:48638096-48638110 chr4:48638159-48638177 chr4:48638095-48638111 chr4:48638095-48638112

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48627219..48628721-chr4:48636980..48639563,2	K562	blood:

Variant related genes	Relation type
FRYL	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10517225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938540	0.86[ASW][hapmap];1.00[MKK][hapmap]
rs11727472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498166	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505376	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12506770	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508327	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13110719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134960	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517675	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1565218	0.91[ASN][1000 genomes]
rs16861344	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1702795	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs1702800	1.00[ASW][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712762	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17609740	1.00[ASN][1000 genomes]
rs17609761	1.00[ASN][1000 genomes]
rs17656189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656212	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656255	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814784	0.93[AMR][1000 genomes]
rs1850520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304387	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs28581223	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945331	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3107023	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695389	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55730515	0.91[ASN][1000 genomes]
rs55884608	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55986500	0.91[ASN][1000 genomes]
rs57893769	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447648	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852840	0.91[ASN][1000 genomes]
rs707719	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814762	0.91[ASN][1000 genomes]
rs73814763	0.91[ASN][1000 genomes]
rs73814782	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814798	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817807	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817808	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817809	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817826	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817827	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7436127	0.86[ASW][hapmap];1.00[MKK][hapmap]
rs7667909	0.85[MKK][hapmap]
rs7690681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693468	0.91[ASN][1000 genomes]
rs7695730	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776581	0.84[ASW][hapmap]
rs776582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776593	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776596	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776598	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776599	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938790	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
5	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48575200-48643000	Weak transcription	HSMMtube	muscle
2	chr4:48588400-48644600	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:48597800-48644600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:48606800-48645000	Weak transcription	Gastric	stomach
5	chr4:48620200-48644800	Weak transcription	Fetal Stomach	stomach
6	chr4:48621200-48642400	Weak transcription	Fetal Heart	heart
7	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
8	chr4:48621800-48642200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:48621800-48645000	Weak transcription	Lung	lung
10	chr4:48621800-48655800	Weak transcription	Colonic Mucosa	Colon
11	chr4:48622800-48644800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:48622800-48648400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:48623400-48644400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:48625800-48642000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:48627200-48645000	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:48627200-48652400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:48627200-48656400	Weak transcription	Fetal Intestine Small	intestine
18	chr4:48632200-48644800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:48635200-48644800	Weak transcription	Aorta	Aorta
20	chr4:48635200-48654000	Weak transcription	Fetal Intestine Large	intestine
21	chr4:48635200-48655000	Weak transcription	Dnd41	blood
22	chr4:48636000-48638400	Enhancers	A549	lung
23	chr4:48636200-48642600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:48636200-48642600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:48636400-48642800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:48636400-48643000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:48636600-48638600	Enhancers	Primary B cells from cord blood	blood
28	chr4:48636800-48638400	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr4:48636800-48638600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:48636800-48639600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr4:48637000-48638400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:48637000-48638600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:48637200-48638400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:48637200-48638400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr4:48637200-48638400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr4:48637200-48638600	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr4:48637400-48638400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:48637600-48638400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:48637600-48639600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr4:48637600-48656400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr4:48637800-48638400	Enhancers	Brain Hippocampus Middle	brain
42	chr4:48637800-48638600	Enhancers	GM12878-XiMat	blood
43	chr4:48637800-48638600	Enhancers	NHEK	skin
44	chr4:48637800-48639000	Weak transcription	Primary T cells from cord blood	blood
45	chr4:48637800-48639400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:48637800-48640000	Weak transcription	Brain Anterior Caudate	brain
47	chr4:48637800-48641200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:48637800-48641800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:48637800-48642000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr4:48637800-48642000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links