Variant report

Variant	rs10874753
Chromosome Location	chr1:93429087-93429088
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr1:93429081-93429093	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:93425643-93429210	GM12891	blood:	n/a	n/a
3	MTA3	chr1:93425510-93429172	GM12878	blood:	n/a	n/a
4	MXI1	chr1:93425648-93429246	SK-N-SH	brain:	n/a	n/a
5	ZNF263	chr1:93428791-93429317	HEK293-T-REx	kidney:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93428117..93429773-chr1:93455192..93456852,2	K562	blood:
2	chr1:93427351..93429788-chr1:93458702..93460989,2	MCF-7	breast:
3	chr1:93296356..93298770-chr1:93426282..93429088,3	MCF-7	breast:
4	chr1:93425058..93429733-chr1:93431759..93435608,8	K562	blood:
5	chr1:93418758..93421387-chr1:93428230..93431121,2	MCF-7	breast:
6	chr1:93428670..93431519-chr1:93436663..93439033,2	MCF-7	breast:

No data

Variant related genes	Relation type
FAM69A	TF binding region
ENSG00000252121	Chromatin interaction
ENSG00000122406	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10493863	0.83[CEU][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10782945	0.87[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs10782946	0.87[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs10874744	0.87[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs10874746	0.87[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap]
rs10874747	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs10874751	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11164830	0.85[EUR][1000 genomes]
rs11164835	0.92[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164836	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164840	0.93[EUR][1000 genomes]
rs11164842	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164843	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164844	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164845	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164857	1.00[JPT][hapmap]
rs11577636	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11578986	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11583491	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11587920	0.95[EUR][1000 genomes]
rs12059883	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12060952	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12065253	0.95[EUR][1000 genomes]
rs12066638	0.92[CEU][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs12069727	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12074608	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12081675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12745968	0.92[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1360366	0.87[CEU][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs17380908	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2255717	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2255723	0.92[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2263247	0.92[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs2391177	0.92[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs2481710	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2481711	0.88[EUR][1000 genomes]
rs2481712	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs2481713	0.92[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs2481714	0.85[EUR][1000 genomes]
rs2492293	0.83[EUR][1000 genomes]
rs2492294	0.89[EUR][1000 genomes]
rs2774945	0.89[EUR][1000 genomes]
rs2774946	0.88[EUR][1000 genomes]
rs2774949	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2774950	0.89[EUR][1000 genomes]
rs2774952	0.89[EUR][1000 genomes]
rs2774953	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2774954	0.92[EUR][1000 genomes]
rs2774955	0.85[EUR][1000 genomes]
rs2774956	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs2811589	0.93[EUR][1000 genomes]
rs2811590	0.93[EUR][1000 genomes]
rs2811591	0.91[EUR][1000 genomes]
rs2811593	0.92[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs2811594	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2811596	0.89[EUR][1000 genomes]
rs2811597	0.88[EUR][1000 genomes]
rs2811598	0.89[EUR][1000 genomes]
rs2811600	0.92[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2893225	0.88[EUR][1000 genomes]
rs34084844	0.94[EUR][1000 genomes]
rs34389767	0.91[EUR][1000 genomes]
rs34398175	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35367625	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35807969	0.89[EUR][1000 genomes]
rs4300228	0.87[EUR][1000 genomes]
rs4351651	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4420089	0.94[EUR][1000 genomes]
rs4450029	0.95[EUR][1000 genomes]
rs4561051	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4592265	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4847378	0.92[CEU][hapmap]
rs4847384	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs56193705	0.89[EUR][1000 genomes]
rs6604028	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6604029	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6604030	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6604031	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs6666223	0.85[EUR][1000 genomes]
rs6694051	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6697543	0.84[EUR][1000 genomes]
rs6698082	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6698179	0.95[EUR][1000 genomes]
rs6698233	0.92[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs6700585	0.88[EUR][1000 genomes]
rs7417198	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7515257	0.92[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7517935	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7536563	0.87[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs7542608	0.92[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7543548	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7550347	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7550660	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9439948	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs9440127	0.87[EUR][1000 genomes]
rs9440134	0.93[EUR][1000 genomes]
rs949915	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs9651257	0.92[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10874753	BARHL2	cis	parietal	SCAN
rs10874753	KIAA1107	cis	cerebellum	SCAN
rs10874753	MTF2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93427800-93429200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
2	chr1:93427800-93433800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:93428000-93429200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:93428000-93429200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:93428000-93429200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:93428000-93429200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:93428000-93429400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr1:93428000-93430200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr1:93428000-93431600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:93428000-93431800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:93428000-93432200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:93428000-93434200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:93428200-93429200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:93428200-93429200	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr1:93428200-93430200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:93428200-93431400	Enhancers	Primary B cells from peripheral blood	blood
17	chr1:93428200-93431400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:93428200-93431600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:93428200-93432000	Enhancers	Fetal Thymus	thymus
20	chr1:93428200-93432200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:93428200-93432200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:93428200-93433600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:93428200-93433600	Weak transcription	Hela-S3	cervix
24	chr1:93428200-93438400	Weak transcription	Brain Angular Gyrus	brain
25	chr1:93428400-93429200	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr1:93428400-93429200	Enhancers	K562	blood
27	chr1:93428400-93430200	Weak transcription	Small Intestine	intestine
28	chr1:93428400-93430800	Enhancers	Dnd41	blood
29	chr1:93428400-93431000	Enhancers	Primary B cells from cord blood	blood
30	chr1:93428400-93433600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:93428400-93433600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:93428400-93433600	Weak transcription	Brain Anterior Caudate	brain
33	chr1:93428400-93433600	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:93428400-93433600	Weak transcription	Fetal Heart	heart
35	chr1:93428400-93435000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:93428400-93438200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:93428400-93445800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:93428600-93429800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:93428600-93430000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:93428600-93430200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:93428600-93431600	Enhancers	Thymus	Thymus
42	chr1:93428600-93436800	Weak transcription	NHEK	skin
43	chr1:93428800-93429400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
44	chr1:93428800-93429800	Enhancers	Primary T cells from cord blood	blood
45	chr1:93429000-93429200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:93429000-93429200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:93429000-93429200	Flanking Active TSS	GM12878-XiMat	blood
48	chr1:93429000-93432200	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links