Variant report

Variant	rs2128275
Chromosome Location	chr12:40421985-40421986
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40419862..40422582-chr12:40493466..40495715,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10784338	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10784353	0.82[ASN][1000 genomes]
rs10784356	0.81[ASN][1000 genomes]
rs10784359	0.94[ASN][1000 genomes]
rs10877990	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10878031	0.82[ASN][1000 genomes]
rs10878049	0.94[ASN][1000 genomes]
rs10878089	0.88[ASN][1000 genomes]
rs11174670	0.80[ASN][1000 genomes]
rs11174702	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11174809	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11174812	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174813	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175024	0.88[ASN][1000 genomes]
rs12813098	0.90[ASN][1000 genomes]
rs12823555	0.90[ASN][1000 genomes]
rs2128277	0.87[ASN][1000 genomes]
rs2896825	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3925535	0.92[ASN][1000 genomes]
rs4625545	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767960	0.90[ASN][1000 genomes]
rs6581504	0.88[ASN][1000 genomes]
rs7139216	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs716268	0.88[ASN][1000 genomes]
rs7313209	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313231	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953129	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7954875	0.80[ASN][1000 genomes]
rs7959498	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970812	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9669240	0.88[ASN][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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2128275	AC079630.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40402200-40425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:40405400-40445200	Weak transcription	K562	blood
4	chr12:40405800-40425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:40405800-40426000	Weak transcription	Pancreas	Pancrea
6	chr12:40406000-40423200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:40406600-40423200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:40406600-40425800	Weak transcription	Liver	Liver
9	chr12:40407800-40426000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:40409600-40426000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:40410000-40422200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:40411400-40428200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:40411400-40428600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:40411600-40422000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:40411600-40424000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:40411600-40425600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:40411600-40426200	Weak transcription	Esophagus	oesophagus
18	chr12:40411800-40425200	Weak transcription	Fetal Intestine Small	intestine
19	chr12:40411800-40425600	Weak transcription	Fetal Intestine Large	intestine
20	chr12:40411800-40425600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:40411800-40426400	Weak transcription	Right Ventricle	heart
22	chr12:40415000-40426000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:40416200-40425400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:40416600-40425400	Weak transcription	Psoas Muscle	Psoas
25	chr12:40416600-40441800	Weak transcription	Ovary	ovary
26	chr12:40417000-40426000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:40417000-40426400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:40417200-40423000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:40417200-40425200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:40417200-40425400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:40417200-40425600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:40419000-40428600	Weak transcription	Aorta	Aorta
33	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
34	chr12:40420800-40423200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:40420800-40426000	Weak transcription	Fetal Kidney	kidney
36	chr12:40421200-40422400	Enhancers	HMEC	breast
37	chr12:40421200-40422600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:40421400-40422200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:40421600-40427000	Weak transcription	Brain Anterior Caudate	brain
40	chr12:40421600-40428000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
42	chr12:40421800-40427800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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