Variant report

Variant	rs1196870
Chromosome Location	chr12:105564229-105564230
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105558828..105561885-chr12:105562217..105566116,3	MCF-7	breast:
2	chr12:105564104..105568210-chr12:105569076..105573485,6	MCF-7	breast:
3	chr12:105557729..105562363-chr12:105563109..105566794,6	K562	blood:
4	chr12:105561858..105564430-chr12:105566394..105568503,2	MCF-7	breast:
5	chr12:105562609..105564624-chr12:105567516..105570192,2	K562	blood:
6	chr12:105558800..105560574-chr12:105563274..105565679,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11112414	0.80[ASN][1000 genomes]
rs11610656	0.84[ASN][1000 genomes]
rs1196750	0.86[ASN][1000 genomes]
rs1196751	0.81[EUR][1000 genomes]
rs1196766	0.84[ASN][1000 genomes]
rs1196767	0.84[ASN][1000 genomes]
rs1196803	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196804	0.99[ASN][1000 genomes]
rs1196809	0.98[ASN][1000 genomes]
rs1196810	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196812	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196814	0.98[ASN][1000 genomes]
rs1196816	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196821	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1196822	0.96[ASN][1000 genomes]
rs1196826	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196827	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196828	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196829	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196835	0.92[ASN][1000 genomes]
rs1196836	0.95[ASN][1000 genomes]
rs1196837	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196838	0.95[ASN][1000 genomes]
rs1196840	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196843	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1196846	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196850	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1196854	0.96[ASN][1000 genomes]
rs1196855	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1196856	0.96[ASN][1000 genomes]
rs1196858	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196860	0.96[ASN][1000 genomes]
rs1196865	0.97[ASN][1000 genomes]
rs1196866	0.97[ASN][1000 genomes]
rs1196867	0.97[ASN][1000 genomes]
rs1196868	0.98[ASN][1000 genomes]
rs1196876	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196877	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196878	0.99[ASN][1000 genomes]
rs1201657	0.94[ASN][1000 genomes]
rs1201658	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732371	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1732378	0.94[ASN][1000 genomes]
rs1732379	0.94[ASN][1000 genomes]
rs1732384	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2264066	0.96[ASN][1000 genomes]
rs2440713	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440717	0.99[ASN][1000 genomes]
rs2440719	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9143	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	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	esv1826054	chr12:105505809-105568176	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1049296	chr12:105518764-105566079	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv870352	chr12:105557770-105589263	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105505200-105567400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:105505200-105573000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:105505600-105573200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:105505800-105571400	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr12:105506400-105573000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:105506800-105568800	Strong transcription	Dnd41	blood
7	chr12:105506800-105572400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr12:105507000-105573200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:105507200-105571400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr12:105507400-105565600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr12:105507600-105571400	Strong transcription	HUVEC	blood vessel
12	chr12:105507600-105572800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:105507800-105573200	Strong transcription	Placenta	Placenta
14	chr12:105508000-105565400	Strong transcription	Adipose Nuclei	Adipose
15	chr12:105508200-105572800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:105508600-105573000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:105508800-105565000	Strong transcription	Liver	Liver
18	chr12:105510000-105565200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:105513800-105567800	Weak transcription	Pancreas	Pancrea
20	chr12:105518600-105573200	Strong transcription	HSMM	muscle
21	chr12:105522600-105586000	Weak transcription	Stomach Mucosa	stomach
22	chr12:105524600-105578200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:105525400-105583200	Weak transcription	Fetal Heart	heart
24	chr12:105527200-105565400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:105529800-105571400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:105532400-105577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:105533200-105565200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:105539800-105565800	Strong transcription	Osteobl	bone
29	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:105549200-105567400	Weak transcription	Fetal Brain Male	brain
31	chr12:105549200-105567800	Weak transcription	Esophagus	oesophagus
32	chr12:105549800-105567200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:105549800-105567200	Weak transcription	Brain Angular Gyrus	brain
34	chr12:105551000-105565200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:105551000-105565600	Strong transcription	NH-A	brain
36	chr12:105552000-105565200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:105553400-105564600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:105555200-105573200	Strong transcription	A549	lung
39	chr12:105556200-105583400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr12:105557400-105571600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:105557600-105565000	Strong transcription	GM12878-XiMat	blood
42	chr12:105557600-105567200	Weak transcription	Fetal Intestine Small	intestine
43	chr12:105557600-105578000	Weak transcription	Gastric	stomach
44	chr12:105558000-105567800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:105558200-105566800	Weak transcription	Colonic Mucosa	Colon
46	chr12:105558200-105567200	Weak transcription	Aorta	Aorta
47	chr12:105558200-105567800	Weak transcription	Lung	lung
48	chr12:105558200-105578200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:105558200-105578400	Weak transcription	Right Ventricle	heart
50	chr12:105558200-105587200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links