Variant report

Variant	rs10861297
Chromosome Location	chr12:105351186-105351187
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:105351138..105353772-chr12:105378582..105380234,3	MCF-7	breast:
2	chr12:105349646..105353787-chr12:105376379..105382982,10	MCF-7	breast:
3	chr12:105318476..105323326-chr12:105350867..105355215,4	MCF-7	breast:
4	chr12:105343851..105348812-chr12:105350003..105354386,8	MCF-7	breast:
5	chr12:105345347..105347103-chr12:105350407..105353151,2	MCF-7	breast:
6	chr12:105290364..105293204-chr12:105349716..105351702,2	MCF-7	breast:
7	chr12:104349867..104352216-chr12:105350654..105352678,2	MCF-7	breast:
8	chr12:105344565..105347442-chr12:105349621..105353002,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265054	Chromatin interaction
ENSG00000136052	Chromatin interaction
ENSG00000151131	Chromatin interaction
ENSG00000204954	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10507183	0.86[ASN][1000 genomes]
rs10507185	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10778354	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10778356	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861278	0.85[ASN][1000 genomes]
rs10861280	0.82[ASN][1000 genomes]
rs10861282	0.91[ASN][1000 genomes]
rs10861291	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861293	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861295	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11112208	0.86[ASN][1000 genomes]
rs11112221	0.86[ASN][1000 genomes]
rs11112234	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12230601	0.80[EUR][1000 genomes]
rs12230637	0.91[ASN][1000 genomes]
rs17829927	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2047126	0.84[ASN][1000 genomes]
rs2245695	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2249941	0.92[ASN][1000 genomes]
rs2252843	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2264883	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2264893	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2453163	0.86[ASN][1000 genomes]
rs2453164	0.86[ASN][1000 genomes]
rs2453169	0.84[ASN][1000 genomes]
rs2463430	0.81[ASN][1000 genomes]
rs2468088	0.80[ASN][1000 genomes]
rs2468094	0.82[ASN][1000 genomes]
rs2468096	0.85[ASN][1000 genomes]
rs2468098	0.85[ASN][1000 genomes]
rs2468103	0.86[ASN][1000 genomes]
rs2468107	0.86[ASN][1000 genomes]
rs2468108	0.86[ASN][1000 genomes]
rs2468336	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2468338	0.84[ASN][1000 genomes]
rs2468339	0.84[ASN][1000 genomes]
rs2468341	0.86[ASN][1000 genomes]
rs2468342	0.82[ASN][1000 genomes]
rs2468343	0.86[ASN][1000 genomes]
rs2468344	0.80[ASN][1000 genomes]
rs2468345	0.82[ASN][1000 genomes]
rs2468396	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2468397	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2642119	0.86[ASN][1000 genomes]
rs2642120	0.86[ASN][1000 genomes]
rs2730294	0.86[ASN][1000 genomes]
rs4130161	0.98[ASN][1000 genomes]
rs4257060	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4409923	0.80[EUR][1000 genomes]
rs4537841	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4630370	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4644704	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57987047	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7959777	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7961766	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7971260	0.86[ASN][1000 genomes]
rs7971392	0.88[ASN][1000 genomes]
rs9705471	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105346800-105351400	Weak transcription	Small Intestine	intestine
2	chr12:105347400-105351400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:105350400-105351200	Enhancers	Muscle Satellite Cultured Cells	--
4	chr12:105350400-105353400	Active TSS	Aorta	Aorta
5	chr12:105350600-105351200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:105350600-105351200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:105350600-105351200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:105350600-105351200	Flanking Active TSS	A549	lung
9	chr12:105350600-105351200	Enhancers	HSMMtube	muscle
10	chr12:105350600-105351400	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:105350600-105351400	Active TSS	Fetal Stomach	stomach
12	chr12:105350600-105351600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:105350600-105351600	Flanking Active TSS	Liver	Liver
14	chr12:105350600-105351600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr12:105350600-105352000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr12:105350600-105352400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:105350600-105352400	Active TSS	Gastric	stomach
18	chr12:105350600-105352600	Active TSS	Duodenum Mucosa	Duodenum
19	chr12:105350600-105352600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr12:105350600-105352600	Active TSS	NHLF	lung
21	chr12:105350600-105353400	Active TSS	Ovary	ovary
22	chr12:105350800-105351200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:105350800-105351200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:105350800-105351200	Active TSS	Brain Germinal Matrix	brain
25	chr12:105350800-105351200	Enhancers	Hela-S3	cervix
26	chr12:105350800-105351200	Enhancers	HSMM	muscle
27	chr12:105350800-105351200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
28	chr12:105350800-105351400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr12:105350800-105351400	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr12:105350800-105351400	Flanking Active TSS	Fetal Brain Female	brain
31	chr12:105350800-105351400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr12:105350800-105351400	Bivalent Enhancer	Dnd41	blood
33	chr12:105350800-105351600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:105350800-105351600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr12:105350800-105351600	Flanking Active TSS	Osteobl	bone
36	chr12:105350800-105351800	Active TSS	Colonic Mucosa	Colon
37	chr12:105350800-105351800	Bivalent Enhancer	Fetal Lung	lung
38	chr12:105350800-105352400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:105350800-105352400	Active TSS	Brain Angular Gyrus	brain
40	chr12:105350800-105352400	Active TSS	Brain Substantia Nigra	brain
41	chr12:105350800-105352400	Active TSS	Stomach Smooth Muscle	stomach
42	chr12:105350800-105352600	Active TSS	Brain Cingulate Gyrus	brain
43	chr12:105350800-105352600	Active TSS	Brain Hippocampus Middle	brain
44	chr12:105350800-105352600	Active TSS	NHDF-Ad	bronchial
45	chr12:105350800-105352800	Active TSS	Rectal Smooth Muscle	rectum
46	chr12:105350800-105353000	Active TSS	Brain Anterior Caudate	brain
47	chr12:105351000-105351200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr12:105351000-105351200	Bivalent Enhancer	Primary B cells from cord blood	blood
49	chr12:105351000-105351200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr12:105351000-105351200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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