Variant report

Variant	rs61943538
Chromosome Location	chr12:118617367-118617368
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	chr12:118617221..118623793-chr12:118809136..118815784,15	MCF-7	breast:
2	chr12:118616609..118618559-chr12:118621695..118624437,2	K562	blood:

Variant related genes	Relation type
ENSG00000270482	Chromatin interaction
ENSG00000111707	Chromatin interaction
ENSG00000135090	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10507286	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068891	0.80[EUR][1000 genomes]
rs16948193	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948197	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948204	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948230	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948234	0.87[EUR][1000 genomes]
rs17433217	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440315	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17440336	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17440364	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440433	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440669	0.82[EUR][1000 genomes]
rs17440774	0.81[EUR][1000 genomes]
rs17512142	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512177	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512198	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512219	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512525	0.82[EUR][1000 genomes]
rs17586342	0.80[EUR][1000 genomes]
rs2280711	0.84[EUR][1000 genomes]
rs3852531	1.00[ASN][1000 genomes]
rs3852532	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55833534	0.87[EUR][1000 genomes]
rs56033674	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56708462	0.87[EUR][1000 genomes]
rs58113338	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58884645	0.80[EUR][1000 genomes]
rs61943364	0.84[EUR][1000 genomes]
rs61943523	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61943524	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61943525	0.91[AMR][1000 genomes]
rs61943528	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61943535	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943537	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945175	0.84[EUR][1000 genomes]
rs61945176	0.84[EUR][1000 genomes]
rs61945177	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945180	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945181	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945182	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945183	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945184	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945187	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945188	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945189	1.00[ASN][1000 genomes]
rs61945190	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945192	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945206	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945210	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945212	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945216	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945217	1.00[ASN][1000 genomes]
rs61945218	0.87[EUR][1000 genomes]
rs61945219	0.80[EUR][1000 genomes]
rs61945220	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945221	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945226	0.85[EUR][1000 genomes]
rs61945228	0.83[EUR][1000 genomes]
rs61946067	0.81[EUR][1000 genomes]
rs61946068	0.82[EUR][1000 genomes]
rs7136216	0.91[EUR][1000 genomes]
rs7301950	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303417	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307393	0.82[EUR][1000 genomes]
rs7309671	0.82[EUR][1000 genomes]
rs7314987	1.00[ASN][1000 genomes]
rs73205512	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73205526	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73205531	0.87[EUR][1000 genomes]
rs73220119	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73222058	0.80[EUR][1000 genomes]
rs7954330	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962185	0.85[EUR][1000 genomes]
rs7963353	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963464	0.80[EUR][1000 genomes]
rs7965350	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970481	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974718	0.80[EUR][1000 genomes]
rs7977403	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9669004	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1054703	chr12:118575000-118638613	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv541611	chr12:118575000-118638613	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1035497	chr12:118599539-118732144	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv541612	chr12:118599539-118732144	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118576000-118619600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr12:118576000-118624000	Weak transcription	Stomach Mucosa	stomach
3	chr12:118584000-118627600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:118585800-118619000	Weak transcription	HepG2	liver
5	chr12:118586200-118619400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:118587600-118619200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:118587800-118620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:118589600-118619000	Weak transcription	A549	lung
9	chr12:118592600-118619400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:118593200-118619200	Strong transcription	Fetal Brain Female	brain
11	chr12:118593200-118619400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:118593200-118619600	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr12:118598200-118620000	Weak transcription	Hela-S3	cervix
14	chr12:118599800-118625600	Weak transcription	Pancreas	Pancrea
15	chr12:118602200-118619600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:118602200-118619600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:118602400-118619600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:118602600-118619600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:118602800-118619600	Strong transcription	Primary T cells from cord blood	blood
20	chr12:118602800-118619600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:118603200-118619600	Strong transcription	Brain Anterior Caudate	brain
22	chr12:118603600-118625400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:118603800-118619400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:118604000-118619600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:118604400-118617400	Strong transcription	Dnd41	blood
26	chr12:118604400-118619600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:118604400-118619600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr12:118604600-118619200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:118604800-118619400	Strong transcription	Fetal Intestine Large	intestine
30	chr12:118605400-118619600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:118605600-118617400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:118607000-118619400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:118607000-118619400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:118607000-118619400	Strong transcription	Adipose Nuclei	Adipose
35	chr12:118607200-118617400	Strong transcription	Thymus	Thymus
36	chr12:118607200-118619400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr12:118607200-118619600	Strong transcription	Brain Cingulate Gyrus	brain
38	chr12:118607200-118619600	Strong transcription	Fetal Stomach	stomach
39	chr12:118607200-118619600	Strong transcription	Fetal Thymus	thymus
40	chr12:118607400-118619200	Strong transcription	Brain Angular Gyrus	brain
41	chr12:118607400-118619200	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr12:118607400-118619400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:118607400-118619600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr12:118607600-118619400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:118607600-118619600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:118607800-118619400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:118607800-118619400	Strong transcription	Left Ventricle	heart
48	chr12:118607800-118619400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr12:118607800-118619600	Strong transcription	Fetal Muscle Leg	muscle
50	chr12:118607800-118619600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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