Variant report

Variant	rs61101304
Chromosome Location	chr12:39697299-39697300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39690972..39693239-chr12:39694761..39697625,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11171568	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171662	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11171666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171669	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11171691	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171786	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11171794	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11171797	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11171834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11171844	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11171857	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172109	0.92[AFR][1000 genomes]
rs11172263	0.83[EUR][1000 genomes]
rs12227642	0.84[ASN][1000 genomes]
rs12228664	0.83[EUR][1000 genomes]
rs12231250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12231735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17127036	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17127059	0.92[AFR][1000 genomes]
rs17127072	0.92[AFR][1000 genomes]
rs17127115	0.92[AFR][1000 genomes]
rs56154721	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56326136	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56885420	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57785083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58125663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58648215	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61453715	0.92[AFR][1000 genomes]
rs7964039	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788260	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899013	chr12:39567945-39732430	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv470286	chr12:39651893-39729700	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39682000-39699200	Weak transcription	Hela-S3	cervix
2	chr12:39685200-39697400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:39685200-39714400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:39686400-39699600	Weak transcription	HMEC	breast
5	chr12:39686600-39722400	Weak transcription	GM12878-XiMat	blood
6	chr12:39686600-39725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:39686800-39729800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:39686800-39738800	Weak transcription	Pancreas	Pancrea
9	chr12:39687200-39726400	Weak transcription	Fetal Intestine Small	intestine
10	chr12:39687600-39723800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:39688400-39709800	Weak transcription	Ovary	ovary
12	chr12:39688400-39724600	Weak transcription	Esophagus	oesophagus
13	chr12:39688400-39726400	Weak transcription	Aorta	Aorta
14	chr12:39688800-39698200	Weak transcription	Brain Substantia Nigra	brain
15	chr12:39689000-39697800	Weak transcription	Brain Angular Gyrus	brain
16	chr12:39689000-39698400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:39689000-39699600	Weak transcription	Fetal Heart	heart
18	chr12:39689000-39724000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:39689600-39699000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:39689600-39702200	Weak transcription	Right Ventricle	heart
21	chr12:39689600-39725400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:39690400-39703000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:39690400-39715200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:39690600-39701400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:39690600-39711600	Weak transcription	Placenta	Placenta
26	chr12:39690800-39697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:39690800-39700800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:39690800-39704400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:39691800-39703400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:39692400-39697800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:39693800-39705600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:39694000-39697800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:39694000-39699800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:39694600-39697800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:39694800-39697400	Enhancers	Fetal Lung	lung
36	chr12:39694800-39697600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:39694800-39699800	Weak transcription	HSMM	muscle
38	chr12:39695000-39726400	Weak transcription	Fetal Intestine Large	intestine
39	chr12:39695000-39726400	Weak transcription	HepG2	liver
40	chr12:39695200-39699400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr12:39695200-39701200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr12:39695400-39700400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:39695400-39701600	Strong transcription	A549	lung
44	chr12:39695400-39701800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:39695400-39704400	Weak transcription	NHEK	skin
46	chr12:39695600-39697400	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:39695600-39699400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:39695600-39703200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:39695600-39724000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr12:39695600-39742000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links