Variant report

Variant	rs6546887
Chromosome Location	chr2:74250781-74250782
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74229439..74231997-chr2:74248517..74251708,3	K562	blood:
2	chr2:74249742..74252123-chr2:74253295..74256040,2	MCF-7	breast:
3	chr2:74233005..74244618-chr2:74246652..74253562,14	MCF-7	breast:
4	chr2:74229588..74231997-chr2:74249219..74251708,2	K562	blood:

Variant related genes	Relation type
ENSG00000187605	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10164943	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10168249	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10168408	0.96[AFR][1000 genomes];0.95[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	0.86[AMR][1000 genomes];0.87[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];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10198884	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10200470	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11126424	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11884748	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885172	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[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];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11898903	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12328927	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713803	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713804	0.91[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713805	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713806	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713808	0.81[AMR][1000 genomes];0.86[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];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12988533	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12995468	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13005103	0.84[EUR][1000 genomes]
rs13006301	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13006407	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13011961	0.84[EUR][1000 genomes]
rs13013211	0.83[EUR][1000 genomes]
rs13014576	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13016198	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13021880	0.82[AMR][1000 genomes];0.88[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	0.89[EUR][1000 genomes]
rs13387010	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13387412	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs13396777	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs28450901	0.92[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	0.81[EUR][1000 genomes]
rs35592918	0.90[EUR][1000 genomes]
rs35609589	0.91[EUR][1000 genomes]
rs3902790	0.95[CEU][hapmap];0.93[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];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4241260	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4270374	0.86[EUR][1000 genomes]
rs4328662	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4331526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4338985	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4364046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4371381	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374402	0.88[EUR][1000 genomes]
rs4416242	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4422181	0.87[EUR][1000 genomes]
rs4574138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4578887	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4621184	0.81[AMR][1000 genomes];0.88[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];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4853003	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]
rs4853005	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.92[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];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4853007	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4853009	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60279245	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6546884	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6546885	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546886	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546889	1.00[JPT][hapmap]
rs6706327	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6713313	0.92[EUR][1000 genomes]
rs6714186	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6717896	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6741544	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743073	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745236	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745576	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6745792	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.88[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];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6756474	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71337722	0.86[EUR][1000 genomes]
rs7560668	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[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];0.95[YRI][hapmap];0.82[AMR][1000 genomes];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	0.83[AMR][1000 genomes];0.89[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];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7597388	0.84[EUR][1000 genomes]
rs7601526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606491	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9309478	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];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

No data

Chromatin state (count:97 , 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	chr2:74246600-74251800	Enhancers	K562	blood
24	chr2:74246800-74254000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:74247200-74252600	Weak transcription	Fetal Intestine Large	intestine
26	chr2:74247400-74254600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:74248200-74251200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:74248200-74252600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:74248400-74251600	Weak transcription	Primary B cells from cord blood	blood
30	chr2:74248400-74253400	Weak transcription	Colonic Mucosa	Colon
31	chr2:74248400-74258200	Weak transcription	Esophagus	oesophagus
32	chr2:74248600-74250800	Enhancers	Dnd41	blood
33	chr2:74248600-74251200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:74248600-74251200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:74248600-74251200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:74248600-74251400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:74248600-74252800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:74248600-74253000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:74248600-74254800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:74248600-74256000	Weak transcription	Psoas Muscle	Psoas
41	chr2:74248600-74257800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:74248600-74258200	Weak transcription	Spleen	Spleen
43	chr2:74248600-74259000	Weak transcription	HSMM	muscle
44	chr2:74248800-74251200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:74248800-74251200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:74248800-74251400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:74248800-74251400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:74248800-74251400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:74248800-74251400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:74248800-74251400	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links