Variant report

Variant	rs793499
Chromosome Location	chr3:99565576-99565577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99563302..99565936-chr3:99585256..99586921,2	K562	blood:
2	chr3:99558033..99560301-chr3:99564115..99565654,2	MCF-7	breast:
3	chr3:99564424..99566018-chr3:99722701..99724331,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10049383	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1016914	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs1021102	0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap]
rs1021103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10212525	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs1038294	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10511177	0.94[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1087198	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs10936005	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs10936008	0.91[JPT][hapmap]
rs1287283	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs13317017	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs1606481	0.80[CEU][hapmap]
rs16841679	0.81[CHB][hapmap]
rs1688766	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1688771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1688772	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1688782	0.83[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs1711557	0.80[CEU][hapmap]
rs1718246	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17392948	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];0.83[MKK][hapmap]
rs2452320	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs2452321	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs28714363	0.80[EUR][1000 genomes]
rs35521705	0.80[EUR][1000 genomes]
rs4075038	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244711	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs4244713	0.80[GIH][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs4279135	0.80[EUR][1000 genomes]
rs4361315	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap]
rs4479633	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs4571265	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap]
rs4928149	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];0.80[EUR][1000 genomes]
rs4928232	0.91[JPT][hapmap];0.89[YRI][hapmap]
rs4928234	0.82[EUR][1000 genomes]
rs629120	0.84[ASW][hapmap];0.80[CEU][hapmap];1.00[YRI][hapmap]
rs6440938	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs6765027	0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs6799379	0.94[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs6807176	0.88[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs6809988	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs694429	0.84[ASW][hapmap];0.80[CEU][hapmap];1.00[YRI][hapmap]
rs704570	0.81[JPT][hapmap];0.80[YRI][hapmap]
rs704573	0.81[JPT][hapmap]
rs704581	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs704582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704583	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs7609729	1.00[JPT][hapmap]
rs7610486	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs7616988	0.94[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7629426	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7636447	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs7638900	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs792834	0.93[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs793440	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs793445	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793452	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs793453	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs793457	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793460	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793461	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793462	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793463	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793465	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793466	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793467	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs793468	0.83[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs793470	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs793472	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793474	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs793488	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs793492	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793494	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs793495	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap]
rs793496	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793503	0.83[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs796977	0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs796978	0.83[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs809415	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs812657	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs923470	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs923471	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs9810235	0.80[EUR][1000 genomes]
rs9832186	0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs9833888	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs9852435	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9864437	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs9872871	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs9873709	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs9873878	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs9875640	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9878931	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs793499	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99551200-99566000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr3:99557000-99573600	Weak transcription	Small Intestine	intestine
5	chr3:99557200-99567200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:99559000-99578000	Weak transcription	HMEC	breast
7	chr3:99561800-99565800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:99561800-99566600	Enhancers	NHDF-Ad	bronchial
9	chr3:99562000-99565600	Enhancers	HUVEC	blood vessel
10	chr3:99562200-99573200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:99562200-99578000	Weak transcription	NHEK	skin
12	chr3:99562400-99565600	Enhancers	Left Ventricle	heart
13	chr3:99562600-99565800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:99562600-99567000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:99562600-99578200	Weak transcription	Fetal Kidney	kidney
16	chr3:99562800-99566600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:99562800-99567200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:99562800-99569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:99562800-99580200	Weak transcription	Gastric	stomach
20	chr3:99563000-99567000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:99563000-99567200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:99563000-99567200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:99563000-99567400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:99563000-99568000	Enhancers	Rectal Smooth Muscle	rectum
25	chr3:99563000-99575000	Weak transcription	Placenta	Placenta
26	chr3:99563000-99577600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:99563200-99565600	Weak transcription	Fetal Intestine Large	intestine
28	chr3:99563200-99567200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:99563200-99567200	Weak transcription	Fetal Stomach	stomach
30	chr3:99563200-99567200	Weak transcription	Lung	lung
31	chr3:99563200-99567200	Weak transcription	Stomach Mucosa	stomach
32	chr3:99563200-99567600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:99563200-99568000	Enhancers	Colon Smooth Muscle	Colon
34	chr3:99563200-99569200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:99563200-99569400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:99563200-99572200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:99563200-99574800	Weak transcription	Psoas Muscle	Psoas
38	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:99563800-99567000	Weak transcription	HSMM	muscle
40	chr3:99563800-99567200	Weak transcription	Spleen	Spleen
41	chr3:99563800-99574800	Weak transcription	Pancreas	Pancrea
42	chr3:99564000-99565600	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr3:99564000-99565600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:99564000-99565600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:99564200-99566400	Enhancers	NHLF	lung
46	chr3:99564200-99577600	Weak transcription	Primary B cells from cord blood	blood
47	chr3:99564400-99567000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:99564600-99566000	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr3:99564600-99566200	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr3:99564800-99565600	Enhancers	K562	blood

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