Variant report

Variant	rs3900976
Chromosome Location	chr12:121571221-121571222
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	chr12:121569906..121572539-chr12:121647803..121649868,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135124	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10849843	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849845	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849846	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849848	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849849	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849850	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849851	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065428	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11065433	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11065435	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11065436	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11065437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065441	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065443	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11065453	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11065458	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs208292	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2393800	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3861798	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3891262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4077055	0.96[ASN][1000 genomes]
rs4559762	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58717055	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489794	0.94[ASN][1000 genomes]
rs684201	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298521	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7302184	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7310821	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7313004	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7314706	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954687	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv430537	chr12:121487632-121579955	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv899563	chr12:121543011-121600529	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121569800-121571400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:121570000-121571400	Active TSS	Brain Anterior Caudate	brain
3	chr12:121570200-121571600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:121570200-121571600	Enhancers	Small Intestine	intestine
5	chr12:121570200-121571800	Active TSS	Brain Hippocampus Middle	brain
6	chr12:121570200-121573000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr12:121570400-121571400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:121570400-121571400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:121570400-121571400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:121570400-121571400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:121570400-121571400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr12:121570400-121571400	Active TSS	Colon Smooth Muscle	Colon
13	chr12:121570400-121571400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr12:121570400-121571400	Flanking Active TSS	Fetal Lung	lung
15	chr12:121570400-121571400	Flanking Active TSS	Fetal Stomach	stomach
16	chr12:121570400-121571400	Active TSS	Ovary	ovary
17	chr12:121570400-121571400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr12:121570400-121571400	Flanking Active TSS	Right Atrium	heart
19	chr12:121570400-121571400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr12:121570400-121571400	Flanking Active TSS	Thymus	Thymus
21	chr12:121570400-121571400	Flanking Active TSS	HepG2	liver
22	chr12:121570400-121571400	Flanking Active TSS	Osteobl	bone
23	chr12:121570400-121571600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:121570400-121571600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr12:121570400-121571600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr12:121570400-121571600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr12:121570400-121571600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr12:121570400-121571600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr12:121570400-121571600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr12:121570400-121571600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:121570400-121571600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:121570400-121571600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr12:121570400-121571600	Flanking Active TSS	Liver	Liver
34	chr12:121570400-121571600	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr12:121570400-121571600	Enhancers	Fetal Brain Male	brain
36	chr12:121570400-121571600	Flanking Active TSS	NHLF	lung
37	chr12:121570400-121571800	Flanking Active TSS	Dnd41	blood
38	chr12:121570400-121572200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:121570400-121572600	Active TSS	Brain Angular Gyrus	brain
40	chr12:121570600-121571400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
41	chr12:121570600-121571400	Active TSS	H9 Cell Line	embryonic stem cell
42	chr12:121570600-121571400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:121570600-121571400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:121570600-121571400	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr12:121570600-121571400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:121570600-121571400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr12:121570600-121571400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr12:121570600-121571400	Flanking Active TSS	Fetal Brain Female	brain
49	chr12:121570600-121571400	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr12:121570600-121571400	Flanking Active TSS	Fetal Muscle Trunk	muscle

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