Variant report

Variant	rs727888
Chromosome Location	chr12:105618007-105618008
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105616267..105619374-chr12:105619746..105623496,4	MCF-7	breast:
2	chr12:105611067..105613851-chr12:105616365..105618135,2	MCF-7	breast:
3	chr12:105606787..105609967-chr12:105617120..105620044,3	MCF-7	breast:
4	chr12:105604459..105610765-chr12:105612400..105619000,9	MCF-7	breast:
5	chr12:105609229..105612971-chr12:105615964..105620947,4	K562	blood:
6	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235162	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10778374	0.81[ASN][1000 genomes]
rs10778375	0.85[ASN][1000 genomes]
rs10861327	0.85[CEU][hapmap]
rs10861328	0.85[CEU][hapmap]
rs10861329	0.86[CEU][hapmap]
rs10861330	0.86[CEU][hapmap]
rs10861335	0.86[CEU][hapmap]
rs10861336	0.86[CEU][hapmap]
rs1109432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112347	0.85[CEU][hapmap]
rs11112350	0.86[CEU][hapmap]
rs11112351	0.86[CEU][hapmap]
rs11112414	0.91[JPT][hapmap]
rs11112436	0.86[ASN][1000 genomes]
rs11612252	0.86[CEU][hapmap]
rs11613261	0.86[CEU][hapmap]
rs1196750	0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196752	0.80[EUR][1000 genomes]
rs1196758	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs1196766	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196767	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196778	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196779	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196785	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs1196804	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs1196809	0.92[EUR][1000 genomes]
rs1196812	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1196814	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs1196816	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1196822	0.91[EUR][1000 genomes]
rs1196835	0.91[EUR][1000 genomes]
rs1196836	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs1196838	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs1196840	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs1196854	0.93[EUR][1000 genomes]
rs1196856	0.94[EUR][1000 genomes]
rs1196860	0.91[EUR][1000 genomes]
rs1196865	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1196866	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1196867	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196868	0.94[EUR][1000 genomes]
rs1196878	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1196880	0.83[EUR][1000 genomes]
rs1196882	0.89[CEU][hapmap]
rs1201657	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs1201658	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12581638	0.85[CEU][hapmap]
rs1317941	0.87[ASN][1000 genomes]
rs17036869	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs1732378	0.89[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes]
rs1732379	0.94[EUR][1000 genomes]
rs1732384	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs2246510	0.96[CEU][hapmap]
rs2264066	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes]
rs2374448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440708	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440713	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2440717	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs2440719	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs4144468	0.86[CEU][hapmap]
rs4964127	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4964346	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6539196	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308195	0.85[CEU][hapmap]
rs7309320	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969800	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9143	0.90[CHB][hapmap];0.86[JPT][hapmap]

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	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
4	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs727888	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

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	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:105590200-105620000	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:105590400-105618800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr12:105591000-105619400	Strong transcription	Primary T cells from cord blood	blood
8	chr12:105595000-105618800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:105596400-105621800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:105600800-105626800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:105601000-105619200	Weak transcription	GM12878-XiMat	blood
12	chr12:105604400-105618400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:105605600-105628400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:105607200-105618600	Genic enhancers	Fetal Intestine Large	intestine
15	chr12:105608600-105618200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:105609000-105618600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:105609200-105620400	Genic enhancers	Fetal Intestine Small	intestine
18	chr12:105609200-105622400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:105609200-105626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:105609200-105628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:105609400-105618600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:105609400-105619400	Strong transcription	Osteobl	bone
23	chr12:105610200-105618800	Strong transcription	Thymus	Thymus
24	chr12:105610800-105620000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:105611000-105620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:105611000-105620200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:105611200-105620200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:105611200-105621200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:105611200-105628200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:105611400-105619600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:105611400-105621200	Weak transcription	Hela-S3	cervix
32	chr12:105611600-105621200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:105611600-105621600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:105611600-105626200	Weak transcription	Fetal Brain Male	brain
35	chr12:105611800-105621200	Weak transcription	Fetal Kidney	kidney
36	chr12:105612000-105624800	Genic enhancers	NHDF-Ad	bronchial
37	chr12:105612200-105618600	Enhancers	Right Atrium	heart
38	chr12:105612600-105618800	Strong transcription	NHEK	skin
39	chr12:105612800-105618600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:105612800-105624200	Strong transcription	Fetal Stomach	stomach
41	chr12:105613000-105623600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr12:105613200-105618400	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:105613200-105620000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:105613800-105618800	Strong transcription	HSMM	muscle
45	chr12:105613800-105622000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:105614200-105618400	Strong transcription	Dnd41	blood
47	chr12:105614200-105619200	Genic enhancers	Rectal Mucosa Donor 31	rectum
48	chr12:105614400-105619200	Genic enhancers	Left Ventricle	heart
49	chr12:105614800-105618600	Genic enhancers	Brain Anterior Caudate	brain
50	chr12:105615000-105618200	Weak transcription	Psoas Muscle	Psoas

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