Variant report

Variant	rs3751320
Chromosome Location	chr12:104853467-104853468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104831707..104833873-chr12:104852450..104855166,2	K562	blood:
2	chr12:104852839..104855254-chr12:104863893..104866118,2	K562	blood:
3	chr12:104852129..104854253-chr12:104856135..104858649,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NFYB-2	chr12:104852873-104854222	ENSG00000245335

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11112066	0.92[ASN][1000 genomes]
rs4964795	0.94[ASN][1000 genomes]
rs4964797	0.91[CEU][hapmap]
rs7976781	0.94[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	nsv832502	chr12:104833729-104908288	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3751320	GNPTAB	cis	parietal	SCAN
rs3751320	PMCH	cis	cerebellum	SCAN
rs3751320	C12orf48	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104849800-104853600	Active TSS	Right Atrium	heart
2	chr12:104850000-104853600	Active TSS	NHDF-Ad	bronchial
3	chr12:104850000-104853800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:104850200-104853600	Active TSS	Brain Anterior Caudate	brain
5	chr12:104850200-104853800	Active TSS	Primary T killer memory cells from peripheral blood	blood
6	chr12:104850200-104854400	Active TSS	Thymus	Thymus
7	chr12:104850200-104854600	Active TSS	GM12878-XiMat	blood
8	chr12:104850400-104853600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:104850400-104853800	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr12:104850600-104853600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
11	chr12:104850800-104853600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:104850800-104855800	Transcr. at gene 5' and 3'	Dnd41	blood
13	chr12:104852000-104855600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
14	chr12:104852200-104855400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr12:104852400-104853600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr12:104852400-104853600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:104852400-104853600	Flanking Active TSS	HUVEC	blood vessel
18	chr12:104852400-104853600	Flanking Active TSS	NH-A	brain
19	chr12:104852400-104854000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:104852400-104854200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr12:104852400-104855600	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr12:104852600-104853600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
23	chr12:104852600-104853600	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr12:104852600-104853800	Active TSS	Brain Cingulate Gyrus	brain
25	chr12:104852600-104854200	Flanking Active TSS	Fetal Thymus	thymus
26	chr12:104852600-104854400	Active TSS	Colonic Mucosa	Colon
27	chr12:104852600-104854800	Flanking Active TSS	K562	blood
28	chr12:104852600-104855000	Active TSS	Brain Hippocampus Middle	brain
29	chr12:104852800-104853600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr12:104852800-104853600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:104852800-104853600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:104852800-104853600	Active TSS	Brain Angular Gyrus	brain
33	chr12:104852800-104854000	Weak transcription	Spleen	Spleen
34	chr12:104852800-104854200	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr12:104852800-104855000	Active TSS	Duodenum Mucosa	Duodenum
36	chr12:104852800-104857400	Weak transcription	Psoas Muscle	Psoas
37	chr12:104853000-104853600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
38	chr12:104853000-104853600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:104853000-104853600	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr12:104853000-104853800	Flanking Active TSS	HMEC	breast
41	chr12:104853000-104854000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:104853000-104854000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:104853000-104854200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:104853000-104854200	Active TSS	Fetal Brain Female	brain
45	chr12:104853000-104854400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr12:104853000-104854800	Weak transcription	Liver	Liver
47	chr12:104853000-104855400	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr12:104853000-104855400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr12:104853000-104855600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:104853200-104853600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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