Variant report

Variant	rs1005974
Chromosome Location	chr6:144872051-144872052
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144867913..144870322-chr6:144871026..144873651,2	K562	blood:
2	chr6:144865086..144866632-chr6:144871745..144873684,2	MCF-7	breast:
3	chr6:144865762..144868928-chr6:144869239..144873744,4	MCF-7	breast:
4	chr6:144871649..144873268-chr6:144877006..144879337,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1016235	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10434891	0.82[JPT][hapmap]
rs11155357	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11155361	0.83[EUR][1000 genomes]
rs12196553	0.82[JPT][hapmap]
rs12201476	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12204372	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214126	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13191597	0.80[EUR][1000 genomes]
rs13193448	0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs13195928	0.84[EUR][1000 genomes]
rs13198102	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13201946	0.88[ASN][1000 genomes]
rs13203229	0.85[MEX][hapmap];0.87[TSI][hapmap]
rs13203387	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205040	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13207331	0.85[ASN][1000 genomes]
rs1534437	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1554813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1554814	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554816	0.89[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs1590055	0.88[ASN][1000 genomes]
rs17793810	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1830271	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1918744	0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs1918745	0.80[EUR][1000 genomes]
rs2103276	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2178128	0.82[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs34095417	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34504312	0.88[ASN][1000 genomes]
rs34571592	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35866755	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35904953	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811099	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3924656	0.82[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs3924657	0.82[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4052725	0.82[EUR][1000 genomes]
rs4075776	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4146297	0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4401687	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs4582403	0.83[EUR][1000 genomes]
rs56158631	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66905872	0.85[ASN][1000 genomes]
rs6908795	0.81[EUR][1000 genomes]
rs6915390	0.83[EUR][1000 genomes]
rs6918394	0.83[EUR][1000 genomes]
rs6919793	0.80[EUR][1000 genomes]
rs6920388	0.80[EUR][1000 genomes]
rs6924812	0.80[EUR][1000 genomes]
rs6938409	0.81[EUR][1000 genomes]
rs6938455	0.83[EUR][1000 genomes]
rs6938776	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73001731	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73005509	0.88[ASN][1000 genomes]
rs7739143	0.82[JPT][hapmap]
rs7740593	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753246	0.82[JPT][hapmap]
rs9376829	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs9390177	0.84[MEX][hapmap];0.87[TSI][hapmap]
rs9390179	0.88[ASN][1000 genomes]
rs9390180	0.86[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs9403565	0.82[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9403566	0.88[ASN][1000 genomes]
rs9403569	0.85[MEX][hapmap];0.82[TSI][hapmap]
rs9403570	0.82[JPT][hapmap]
rs9497023	0.93[JPT][hapmap]
rs952050	0.84[MEX][hapmap];0.87[TSI][hapmap]
rs952051	0.82[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144807400-144904000	Weak transcription	Brain Substantia Nigra	brain
2	chr6:144812400-144881000	Weak transcription	Stomach Mucosa	stomach
3	chr6:144815200-144881000	Weak transcription	NHEK	skin
4	chr6:144816600-144881400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:144831400-144879000	Strong transcription	Primary B cells from cord blood	blood
6	chr6:144837200-144880800	Weak transcription	Brain Angular Gyrus	brain
7	chr6:144850200-144877400	Weak transcription	HMEC	breast
8	chr6:144850400-144903200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:144850400-144903200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:144850400-144904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:144850600-144881600	Weak transcription	Brain Anterior Caudate	brain
12	chr6:144853600-144896400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:144854400-144873400	Weak transcription	Pancreas	Pancrea
14	chr6:144854600-144881200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:144856000-144875800	Weak transcription	Fetal Heart	heart
16	chr6:144857200-144904000	Weak transcription	Psoas Muscle	Psoas
17	chr6:144858200-144887800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr6:144858600-144879200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr6:144858600-144879400	Strong transcription	HepG2	liver
20	chr6:144859600-144878600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:144860200-144879200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:144861000-144878400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:144861200-144885000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:144861800-144876400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:144862200-144873400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:144862400-144872400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:144864000-144876600	Weak transcription	Gastric	stomach
28	chr6:144864400-144878800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:144864800-144874000	Weak transcription	Lung	lung
30	chr6:144864800-144874200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:144864800-144876400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:144864800-144876400	Weak transcription	Esophagus	oesophagus
33	chr6:144864800-144885200	Weak transcription	Colonic Mucosa	Colon
34	chr6:144864800-144885800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr6:144864800-144899000	Weak transcription	Small Intestine	intestine
36	chr6:144865000-144879600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr6:144865200-144872200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:144866200-144875000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:144866200-144881600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:144867000-144878600	Weak transcription	NHLF	lung
41	chr6:144867400-144872400	Weak transcription	Placenta	Placenta
42	chr6:144867400-144903800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:144868200-144874000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:144868200-144879600	Strong transcription	HUVEC	blood vessel
45	chr6:144868600-144875800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:144869000-144879800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr6:144869400-144873000	Strong transcription	Fetal Muscle Leg	muscle
48	chr6:144869400-144879000	Strong transcription	Fetal Thymus	thymus
49	chr6:144869400-144879200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:144869400-144879400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links