Variant report

Variant	rs1196749
Chromosome Location	chr12:105598672-105598673
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105598232..105600634-chr12:105603530..105606133,2	K562	blood:
2	chr12:105598458..105599984-chr12:105777215..105778784,2	MCF-7	breast:
3	chr12:105589883..105591833-chr12:105596630..105599143,3	K562	blood:
4	chr12:105596446..105601745-chr12:105601750..105606856,8	MCF-7	breast:
5	chr12:105592769..105599626-chr12:105599908..105606799,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10746010	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778368	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778369	0.85[EUR][1000 genomes]
rs10861347	1.00[CHB][hapmap]
rs10861371	1.00[CHB][hapmap]
rs10861400	1.00[CHB][hapmap]
rs10861407	1.00[CHB][hapmap]
rs10861409	1.00[CHB][hapmap]
rs1107755	0.84[EUR][1000 genomes]
rs1107757	0.84[EUR][1000 genomes]
rs11112424	0.84[EUR][1000 genomes]
rs11112434	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs11112467	1.00[ASN][1000 genomes]
rs11112475	1.00[CHB][hapmap]
rs1196742	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196745	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196764	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196765	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196770	0.93[EUR][1000 genomes]
rs1196772	0.93[EUR][1000 genomes]
rs1196777	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs1196780	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1196782	0.84[EUR][1000 genomes]
rs1196786	0.84[EUR][1000 genomes]
rs1196787	0.83[EUR][1000 genomes]
rs1196789	0.83[EUR][1000 genomes]
rs1196793	1.00[CHB][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1196795	0.85[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1196797	0.85[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs1196798	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1196800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196805	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196807	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196808	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196811	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1196813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196818	1.00[CHB][hapmap]
rs1196819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196820	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196823	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196825	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196831	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196833	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196834	0.82[EUR][1000 genomes]
rs1196839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196841	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196844	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196847	0.86[EUR][1000 genomes]
rs1196848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196851	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1196852	1.00[CHB][hapmap]
rs1196853	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196869	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs1196871	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196872	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs1196873	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs1196874	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196881	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196884	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196885	0.84[EUR][1000 genomes]
rs1206559	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209308	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209637	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1211276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211277	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211626	0.84[EUR][1000 genomes]
rs12369709	0.83[EUR][1000 genomes]
rs12814458	0.84[EUR][1000 genomes]
rs12816560	0.85[EUR][1000 genomes]
rs12822081	1.00[CHB][hapmap]
rs1345096	0.88[EUR][1000 genomes]
rs1444610	0.83[EUR][1000 genomes]
rs1621553	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1663565	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732370	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166142	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246243	0.90[EUR][1000 genomes]
rs2257156	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes]
rs2374449	1.00[CEU][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2440692	0.88[EUR][1000 genomes]
rs2440714	0.94[EUR][1000 genomes]
rs2440715	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2440718	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464173	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464175	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2464181	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464182	0.96[EUR][1000 genomes]
rs2888846	1.00[CHB][hapmap]
rs35679386	0.83[EUR][1000 genomes]
rs4356312	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356313	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372534	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545651	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4964122	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964331	1.00[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs6539183	1.00[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs6539186	0.84[EUR][1000 genomes]
rs6539187	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539188	0.87[EUR][1000 genomes]
rs7132040	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.89[EUR][1000 genomes]
rs7132855	1.00[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs71441895	0.93[EUR][1000 genomes]
rs7299225	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7299701	0.86[EUR][1000 genomes]
rs7302174	1.00[CHB][hapmap]
rs7302854	0.84[EUR][1000 genomes]
rs7303961	0.91[EUR][1000 genomes]
rs73181823	0.83[EUR][1000 genomes]
rs7959385	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7963877	1.00[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs873119	0.85[EUR][1000 genomes]
rs935240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935242	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935244	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs935246	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935248	1.00[EUR][1000 genomes]
rs935249	0.99[EUR][1000 genomes]
rs9645791	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1196749	LOC387882	cis	multi-tissue	Pritchard
rs1196749	EID3	cis	lymphoblastoid	seeQTL
rs1196749	ALDH1L2	cis	cerebellum	SCAN
rs1196749	APPL2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105571400-105617800	Weak transcription	K562	blood
4	chr12:105576400-105606000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:105577800-105598800	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr12:105577800-105599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:105577800-105602600	Strong transcription	Fetal Thymus	thymus
10	chr12:105577800-105603600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:105577800-105605400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:105577800-105605600	Strong transcription	Primary B cells from cord blood	blood
13	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr12:105578000-105599200	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr12:105578000-105607400	Strong transcription	Fetal Brain Female	brain
16	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr12:105578400-105602400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:105579000-105605200	Strong transcription	Fetal Muscle Leg	muscle
20	chr12:105579000-105612400	Strong transcription	Stomach Smooth Muscle	stomach
21	chr12:105580200-105613200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:105581200-105602600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:105581200-105605400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:105581800-105602600	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:105581800-105605200	Strong transcription	Brain Germinal Matrix	brain
26	chr12:105582000-105600200	Strong transcription	Fetal Stomach	stomach
27	chr12:105582000-105602600	Strong transcription	Lung	lung
28	chr12:105582000-105603400	Strong transcription	Spleen	Spleen
29	chr12:105582800-105602600	Strong transcription	Thymus	Thymus
30	chr12:105583600-105602600	Strong transcription	Esophagus	oesophagus
31	chr12:105583600-105605600	Strong transcription	Right Ventricle	heart
32	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:105584400-105600200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr12:105585400-105603400	Strong transcription	HSMMtube	muscle
35	chr12:105587400-105609000	Weak transcription	Fetal Brain Male	brain
36	chr12:105587800-105598800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:105589000-105600400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr12:105589000-105600400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr12:105589200-105601000	Weak transcription	Hela-S3	cervix
40	chr12:105589200-105612200	Weak transcription	Psoas Muscle	Psoas
41	chr12:105589400-105608600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:105589400-105612400	Weak transcription	Fetal Heart	heart
43	chr12:105590000-105602600	Strong transcription	Colonic Mucosa	Colon
44	chr12:105590200-105602200	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr12:105590200-105620000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:105590400-105618800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr12:105591000-105619400	Strong transcription	Primary T cells from cord blood	blood
48	chr12:105591400-105599000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:105591600-105600400	Weak transcription	GM12878-XiMat	blood
50	chr12:105592400-105600400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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