Variant report

Variant	rs4853003
Chromosome Location	chr2:74248871-74248872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:74211189..74213598-chr2:74245485..74249167,4	MCF-7	breast:
2	chr2:74245821..74249832-chr2:74253279..74256984,4	MCF-7	breast:
3	chr2:74247761..74249753-chr2:74252824..74255586,3	K562	blood:
4	chr2:74229439..74231997-chr2:74248517..74251708,3	K562	blood:
5	chr2:74239770..74244279-chr2:74244536..74249851,6	K562	blood:
6	chr2:74247578..74249346-chr2:74314396..74316715,2	MCF-7	breast:
7	chr2:74247122..74249502-chr2:74251565..74254079,2	MCF-7	breast:
8	chr2:74233005..74244618-chr2:74246652..74253562,14	MCF-7	breast:
9	chr2:74155178..74157065-chr2:74247210..74249672,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000187605	Chromatin interaction
ENSG00000235499	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10164943	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10168249	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10168408	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10168410	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10179742	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10179967	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10182376	0.86[ASN][1000 genomes]
rs10184542	0.90[ASN][1000 genomes]
rs10191539	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10198884	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10200470	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11126424	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11884748	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885172	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11886928	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11898903	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12328927	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713803	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713804	0.91[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713805	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713806	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713808	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713809	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12713810	0.91[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12988533	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12995468	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13005103	0.85[EUR][1000 genomes]
rs13006301	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13006407	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13011961	0.85[EUR][1000 genomes]
rs13013211	0.83[EUR][1000 genomes]
rs13014576	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13016198	1.00[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs13021880	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13027288	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13027623	0.88[EUR][1000 genomes]
rs13030414	0.90[EUR][1000 genomes]
rs13387010	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13387412	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13396777	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs28450901	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28460865	0.84[ASN][1000 genomes]
rs34136450	0.83[EUR][1000 genomes]
rs34201525	0.82[EUR][1000 genomes]
rs35592918	0.90[EUR][1000 genomes]
rs35609589	0.91[EUR][1000 genomes]
rs3902790	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4073048	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4241260	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4270374	0.86[EUR][1000 genomes]
rs4328662	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4331526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4338985	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4364046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4371381	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374402	0.89[EUR][1000 genomes]
rs4416242	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4422181	0.88[EUR][1000 genomes]
rs4574138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4578887	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4621184	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4852326	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4853005	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4853006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4853007	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4853009	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60279245	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6546884	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6546885	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546886	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546889	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6706327	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6713313	0.92[EUR][1000 genomes]
rs6714186	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6717896	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6741544	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743073	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745236	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745576	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6745792	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6754218	0.86[EUR][1000 genomes]
rs6755711	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6756474	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71337722	0.87[EUR][1000 genomes]
rs7560668	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7568898	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7584777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7587991	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7589915	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7592749	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7593050	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7595401	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7597388	0.85[EUR][1000 genomes]
rs7601526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606491	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9309478	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][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	esv3584956	chr2:74197109-74317135	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv818048	chr2:74225434-74313080	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4853003	SLC4A5	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74231600-74273800	Weak transcription	A549	lung
2	chr2:74235000-74258400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:74235000-74259200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:74236200-74251200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:74236400-74251400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:74236400-74259400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:74237400-74252800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:74237400-74259000	Weak transcription	NHLF	lung
9	chr2:74237600-74251400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:74237600-74251600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:74237600-74252800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:74238000-74252800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:74238600-74251200	Weak transcription	NHEK	skin
14	chr2:74238600-74258400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:74238800-74258200	Weak transcription	Liver	Liver
16	chr2:74238800-74259600	Weak transcription	HMEC	breast
17	chr2:74239000-74251400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:74240000-74276200	Weak transcription	Hela-S3	cervix
19	chr2:74245000-74251400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:74245800-74253400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:74246000-74253400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:74246000-74253400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr2:74246200-74249000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:74246400-74249000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr2:74246400-74249000	Enhancers	Brain Angular Gyrus	brain
26	chr2:74246400-74249000	Enhancers	Brain Cingulate Gyrus	brain
27	chr2:74246400-74249000	Enhancers	Brain Substantia Nigra	brain
28	chr2:74246400-74249000	Enhancers	Fetal Brain Female	brain
29	chr2:74246600-74249000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr2:74246600-74249000	Strong transcription	HepG2	liver
31	chr2:74246600-74249200	Enhancers	Brain Hippocampus Middle	brain
32	chr2:74246600-74249800	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr2:74246600-74251800	Enhancers	K562	blood
34	chr2:74246800-74249000	Enhancers	Primary T cells fromperipheralblood	blood
35	chr2:74246800-74249000	Enhancers	Brain Germinal Matrix	brain
36	chr2:74246800-74249000	Enhancers	Pancreas	Pancrea
37	chr2:74246800-74249000	Enhancers	Right Atrium	heart
38	chr2:74246800-74254000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:74247000-74249000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr2:74247200-74249000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:74247200-74249200	Enhancers	Primary B cells from peripheral blood	blood
42	chr2:74247200-74252600	Weak transcription	Fetal Intestine Large	intestine
43	chr2:74247400-74249000	Enhancers	Adipose Nuclei	Adipose
44	chr2:74247400-74250200	Enhancers	Fetal Thymus	thymus
45	chr2:74247400-74254600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:74247600-74249000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:74247600-74249000	Strong transcription	Fetal Intestine Small	intestine
48	chr2:74247600-74249000	Genic enhancers	Thymus	Thymus
49	chr2:74247600-74249000	Flanking Active TSS	GM12878-XiMat	blood
50	chr2:74247600-74249200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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