Variant report

Variant	rs17096380
Chromosome Location	chr12:46361672-46361673
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46359883..46362173-chr12:46370703..46372664,2	K562	blood:
2	chr12:46353562..46359244-chr12:46361441..46367398,6	K562	blood:
3	chr12:46360643..46362650-chr12:46363534..46365705,2	MCF-7	breast:
4	chr12:46354837..46356506-chr12:46359246..46361993,2	MCF-7	breast:
5	chr12:46361472..46363562-chr12:46382349..46384332,2	K562	blood:
6	chr12:46359963..46361845-chr12:46363690..46365645,2	K562	blood:
7	chr12:46361324..46363006-chr12:46372617..46375436,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10748438	1.00[YRI][hapmap]
rs10880871	0.85[YRI][hapmap]
rs10880880	1.00[LWK][hapmap];0.85[YRI][hapmap]
rs10880884	0.85[YRI][hapmap]
rs11574952	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12314770	1.00[LWK][hapmap]
rs1366024	0.85[YRI][hapmap]
rs1863127	0.90[LWK][hapmap]
rs247930	1.00[LWK][hapmap]
rs35115	0.90[LWK][hapmap]
rs35117	1.00[LWK][hapmap]
rs35121	0.90[LWK][hapmap]
rs35125	1.00[LWK][hapmap]
rs6582574	0.90[LWK][hapmap]
rs7971398	0.86[AMR][1000 genomes];0.91[ASN][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	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv3439887	chr12:46337377-46370366	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17096380	ENDOU	cis	parietal	SCAN
rs17096380	RPAP3	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46299000-46381000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:46319200-46362800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:46329800-46371000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr12:46341800-46365600	Weak transcription	K562	blood
5	chr12:46342000-46362400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:46342000-46362400	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:46342000-46362400	Weak transcription	Pancreas	Pancrea
8	chr12:46342000-46363000	Weak transcription	Fetal Stomach	stomach
9	chr12:46342000-46364000	Weak transcription	Gastric	stomach
10	chr12:46342200-46365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:46342200-46369000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:46342800-46362400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:46343000-46375000	Weak transcription	NHEK	skin
14	chr12:46348600-46366200	Weak transcription	Thymus	Thymus
15	chr12:46349200-46367000	Weak transcription	Fetal Intestine Small	intestine
16	chr12:46352000-46363600	Weak transcription	Aorta	Aorta
17	chr12:46353000-46362400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr12:46355600-46367800	Weak transcription	HMEC	breast
19	chr12:46356400-46369200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:46356600-46374200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:46357000-46364000	Weak transcription	Fetal Intestine Large	intestine
22	chr12:46357000-46366000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:46357000-46371000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:46357000-46380400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:46357200-46367000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:46357200-46369000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:46357600-46364200	Weak transcription	Hela-S3	cervix
28	chr12:46357600-46365800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:46357600-46367000	Weak transcription	HUVEC	blood vessel
30	chr12:46357600-46380000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:46357800-46363400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:46357800-46364000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:46357800-46365200	Weak transcription	Fetal Lung	lung
34	chr12:46357800-46365400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:46357800-46381200	Weak transcription	Fetal Kidney	kidney
36	chr12:46358000-46363000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:46358000-46365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:46358200-46366000	Weak transcription	Placenta	Placenta
39	chr12:46358200-46366200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:46358400-46364600	Enhancers	Fetal Heart	heart
41	chr12:46358600-46363600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr12:46358800-46362200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:46358800-46363600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr12:46358800-46364200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr12:46358800-46365000	Weak transcription	Primary T cells from cord blood	blood
46	chr12:46358800-46365600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:46358800-46380600	Weak transcription	Spleen	Spleen
48	chr12:46359000-46361800	Enhancers	NHDF-Ad	bronchial
49	chr12:46359000-46362600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr12:46359000-46365000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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