Variant report

Variant	rs1196776
Chromosome Location	chr12:105622078-105622079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105501229..105503953-chr12:105621352..105624637,3	MCF-7	breast:
2	chr12:105608225..105613366-chr12:105619333..105624104,5	MCF-7	breast:
3	chr12:105620755..105625323-chr12:105625745..105629848,5	K562	blood:
4	chr12:105499627..105501658-chr12:105620143..105622423,2	K562	blood:
5	chr12:105616267..105619374-chr12:105619746..105623496,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000257999	Chromatin interaction
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10778374	0.81[ASN][1000 genomes]
rs10778375	0.86[ASN][1000 genomes]
rs1109432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112436	0.86[ASN][1000 genomes]
rs1196750	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1196766	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196767	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1196768	0.98[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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196779	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196781	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196785	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196788	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196804	0.91[EUR][1000 genomes]
rs1196809	0.91[EUR][1000 genomes]
rs1196814	0.91[EUR][1000 genomes]
rs1196822	0.90[EUR][1000 genomes]
rs1196835	0.90[EUR][1000 genomes]
rs1196836	0.90[EUR][1000 genomes]
rs1196838	0.88[EUR][1000 genomes]
rs1196854	0.93[EUR][1000 genomes]
rs1196856	0.93[EUR][1000 genomes]
rs1196860	0.90[EUR][1000 genomes]
rs1196866	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1196867	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196868	0.93[EUR][1000 genomes]
rs1196878	0.90[EUR][1000 genomes]
rs1196880	0.82[EUR][1000 genomes]
rs1201657	0.93[EUR][1000 genomes]
rs1317941	0.88[ASN][1000 genomes]
rs17036869	0.85[ASN][1000 genomes]
rs1732378	0.93[EUR][1000 genomes]
rs1732379	0.93[EUR][1000 genomes]
rs2264066	0.93[EUR][1000 genomes]
rs2374448	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440708	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440717	0.91[EUR][1000 genomes]
rs4964127	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4964346	0.90[AMR][1000 genomes];0.91[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]
rs727888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7309320	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310488	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969800	0.92[AMR][1000 genomes];0.91[EUR][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	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
rs1196776	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	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:105600800-105626800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:105605600-105628400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:105609200-105622400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:105609200-105626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:105609200-105628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:105611200-105628200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:105611600-105626200	Weak transcription	Fetal Brain Male	brain
11	chr12:105612000-105624800	Genic enhancers	NHDF-Ad	bronchial
12	chr12:105612800-105624200	Strong transcription	Fetal Stomach	stomach
13	chr12:105613000-105623600	Strong transcription	Fetal Muscle Trunk	muscle
14	chr12:105616400-105623200	Strong transcription	Fetal Brain Female	brain
15	chr12:105616600-105629000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr12:105617000-105623200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr12:105617000-105629000	Weak transcription	Esophagus	oesophagus
18	chr12:105617400-105622800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:105617400-105625400	Genic enhancers	Muscle Satellite Cultured Cells	--
20	chr12:105617400-105629000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:105617600-105625400	Strong transcription	A549	lung
22	chr12:105618200-105625200	Weak transcription	Right Ventricle	heart
23	chr12:105618600-105625200	Weak transcription	Spleen	Spleen
24	chr12:105618600-105626800	Weak transcription	Gastric	stomach
25	chr12:105619200-105623000	Strong transcription	Placenta	Placenta
26	chr12:105619400-105625200	Genic enhancers	HSMM	muscle
27	chr12:105619400-105627400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:105619800-105622600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:105620000-105622400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:105620000-105622800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:105620000-105623000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:105620000-105623000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:105620000-105623200	Strong transcription	Liver	Liver
34	chr12:105620000-105625800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:105620200-105623000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:105620200-105623000	Weak transcription	K562	blood
37	chr12:105620200-105623200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:105620400-105622400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:105620400-105622400	Strong transcription	Fetal Intestine Small	intestine
40	chr12:105620400-105622800	Weak transcription	Aorta	Aorta
41	chr12:105620400-105622800	Strong transcription	NHEK	skin
42	chr12:105620400-105623000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:105620400-105623000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr12:105620400-105623000	Weak transcription	Small Intestine	intestine
45	chr12:105620400-105623000	Strong transcription	Thymus	Thymus
46	chr12:105620400-105624400	Weak transcription	Right Atrium	heart
47	chr12:105620400-105624600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:105620400-105624800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:105620400-105625000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:105620400-105625200	Weak transcription	Primary hematopoietic stem cells	blood

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