Variant report

Variant	rs3741798
Chromosome Location	chr12:12496086-12496087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12492591..12496628-chr12:12508387..12511489,3	K562	blood:
2	chr12:12492591..12498034-chr12:12508387..12511659,4	K562	blood:
3	chr12:12493042..12496407-chr12:12508406..12511511,3	MCF-7	breast:
4	chr12:12493698..12498336-chr12:12499976..12504386,5	MCF-7	breast:
5	chr12:12494246..12497461-chr12:12509029..12511759,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205791	Chromatin interaction
ENSG00000165714	Chromatin interaction
ENSG00000111261	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1544684	0.87[YRI][hapmap]
rs17303178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17375328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2160588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28372890	0.90[EUR][1000 genomes]
rs3825259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865572	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55892345	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56829405	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57725255	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922023	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922024	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922025	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922026	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922027	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922028	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922044	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922045	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922046	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922047	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922049	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922052	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922054	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922057	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73277486	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73277491	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73279305	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980482	1.00[CHB][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898807	chr12:12448948-12502001	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv898809	chr12:12488067-12509314	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3741798	PRL	trans	lymphoblastoid	seeQTL
rs3741798	KIAA1467	cis	cerebellum	SCAN
rs3741798	LOH12CR1	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12473200-12501600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:12473600-12502000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:12473800-12502400	Weak transcription	NHLF	lung
4	chr12:12480400-12502400	Weak transcription	Right Ventricle	heart
5	chr12:12481200-12502200	Weak transcription	Fetal Heart	heart
6	chr12:12481800-12502400	Weak transcription	Psoas Muscle	Psoas
7	chr12:12482400-12502200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:12483600-12502800	Weak transcription	Spleen	Spleen
9	chr12:12485400-12500200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:12485400-12502400	Weak transcription	Esophagus	oesophagus
11	chr12:12485400-12502800	Weak transcription	Gastric	stomach
12	chr12:12485400-12502800	Weak transcription	Small Intestine	intestine
13	chr12:12487200-12502600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:12487400-12502200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:12487400-12502200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:12487600-12502200	Weak transcription	Colonic Mucosa	Colon
17	chr12:12488000-12502000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:12489200-12497600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:12489600-12502400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:12489600-12502600	Weak transcription	Placenta	Placenta
21	chr12:12489800-12502400	Weak transcription	Pancreas	Pancrea
22	chr12:12490800-12502400	Weak transcription	Brain Germinal Matrix	brain
23	chr12:12491200-12496400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr12:12491200-12496400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr12:12492000-12497200	Weak transcription	Stomach Mucosa	stomach
26	chr12:12492000-12502400	Weak transcription	Aorta	Aorta
27	chr12:12492200-12502200	Weak transcription	Primary B cells from cord blood	blood
28	chr12:12492200-12502200	Weak transcription	Primary T cells from cord blood	blood
29	chr12:12492200-12502600	Weak transcription	Lung	lung
30	chr12:12492200-12502800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:12492400-12502000	Weak transcription	HUVEC	blood vessel
32	chr12:12492400-12502600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:12492800-12496200	Strong transcription	Brain Anterior Caudate	brain
34	chr12:12492800-12496400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr12:12492800-12502000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:12493000-12501400	Weak transcription	K562	blood
37	chr12:12493200-12496200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:12493600-12496400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr12:12493600-12496400	Weak transcription	Thymus	Thymus
40	chr12:12494000-12496200	Strong transcription	Brain Hippocampus Middle	brain
41	chr12:12494200-12502200	Weak transcription	Brain Substantia Nigra	brain
42	chr12:12494200-12502600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:12494400-12496200	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr12:12494400-12502800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:12494600-12496200	Strong transcription	Fetal Intestine Large	intestine
46	chr12:12494600-12501800	Weak transcription	Brain Angular Gyrus	brain
47	chr12:12495000-12496400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:12495000-12502000	Weak transcription	Fetal Brain Female	brain
49	chr12:12495200-12496200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:12495200-12500200	Weak transcription	Fetal Intestine Small	intestine

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