Variant report

Variant	rs12693180
Chromosome Location	chr2:180124472-180124473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:180116382..180118315-chr2:180123410..180126262,2	MCF-7	breast:
2	chr2:180122860..180124976-chr2:180127824..180130891,3	MCF-7	breast:
3	chr2:180115892..180117617-chr2:180123291..180126152,2	K562	blood:
4	chr2:180114550..180116150-chr2:180123274..180125911,2	MCF-7	breast:
5	chr2:180120526..180124742-chr2:180127021..180129947,5	K562	blood:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10170430	0.94[ASN][1000 genomes]
rs10196577	0.94[ASN][1000 genomes]
rs10197425	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10208593	0.91[ASN][1000 genomes]
rs10930856	0.81[EUR][1000 genomes]
rs10930857	0.91[ASN][1000 genomes]
rs12693175	0.83[EUR][1000 genomes]
rs12989055	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13022867	0.83[EUR][1000 genomes]
rs13029576	0.83[EUR][1000 genomes]
rs13389956	1.00[ASN][1000 genomes]
rs13404037	0.81[EUR][1000 genomes]
rs13420582	0.94[ASN][1000 genomes]
rs13427714	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17363260	0.81[EUR][1000 genomes]
rs17363267	0.81[EUR][1000 genomes]
rs35539795	0.91[ASN][1000 genomes]
rs56181927	0.83[EUR][1000 genomes]
rs67028844	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
2	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
3	chr2:180112400-180126200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:180112600-180125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:180112600-180126800	Weak transcription	Hela-S3	cervix
6	chr2:180115400-180127600	Weak transcription	NHLF	lung
7	chr2:180117400-180126200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:180117800-180126400	Weak transcription	Small Intestine	intestine
9	chr2:180118000-180125200	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:180118200-180124800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:180118600-180126200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr2:180118800-180127600	Weak transcription	HSMM	muscle
13	chr2:180118800-180128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:180119400-180128200	Weak transcription	Pancreas	Pancrea
15	chr2:180119600-180126200	Weak transcription	Brain Anterior Caudate	brain
16	chr2:180120000-180127400	Weak transcription	Brain Angular Gyrus	brain
17	chr2:180120200-180127200	Weak transcription	Fetal Kidney	kidney
18	chr2:180120200-180127600	Weak transcription	Fetal Stomach	stomach
19	chr2:180120400-180125000	Weak transcription	Right Atrium	heart
20	chr2:180120400-180126800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:180122600-180127400	Enhancers	Adipose Nuclei	Adipose
22	chr2:180123600-180126400	Weak transcription	Fetal Brain Male	brain
23	chr2:180123600-180126800	Weak transcription	Brain Substantia Nigra	brain
24	chr2:180123800-180125000	Weak transcription	GM12878-XiMat	blood
25	chr2:180123800-180125800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:180123800-180127600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:180123800-180127800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:180123800-180127800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:180123800-180128000	Enhancers	Primary B cells from peripheral blood	blood
30	chr2:180124000-180125200	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:180124000-180127400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:180124200-180126400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:180124200-180126400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:180124200-180126400	Enhancers	NHEK	skin
35	chr2:180124400-180124600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr2:180124400-180124600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr2:180124400-180124600	Enhancers	Primary B cells from cord blood	blood
38	chr2:180124400-180124600	Flanking Active TSS	HepG2	liver
39	chr2:180124400-180125200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:180124400-180126000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:180124400-180126600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:180124400-180127000	Enhancers	HMEC	breast
43	chr2:180124400-180127600	Weak transcription	Fetal Intestine Small	intestine

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