Variant report

Variant	rs1922261
Chromosome Location	chr12:104854011-104854012
allele	A/G
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: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10735397	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778334	0.97[EUR][1000 genomes]
rs12299738	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17035655	1.00[CHD][hapmap]
rs3751319	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs3751321	0.93[AFR][1000 genomes]
rs3751322	0.93[LWK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs7135581	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953927	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[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
rs1922261	SPIC	cis	cerebellum	SCAN
rs1922261	CHST11	cis	cerebellum	SCAN
rs1922261	C12orf45	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104850200-104854400	Active TSS	Thymus	Thymus
2	chr12:104850200-104854600	Active TSS	GM12878-XiMat	blood
3	chr12:104850800-104855800	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr12:104852000-104855600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
5	chr12:104852200-104855400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:104852400-104854200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr12:104852400-104855600	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr12:104852600-104854200	Flanking Active TSS	Fetal Thymus	thymus
9	chr12:104852600-104854400	Active TSS	Colonic Mucosa	Colon
10	chr12:104852600-104854800	Flanking Active TSS	K562	blood
11	chr12:104852600-104855000	Active TSS	Brain Hippocampus Middle	brain
12	chr12:104852800-104854200	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr12:104852800-104855000	Active TSS	Duodenum Mucosa	Duodenum
14	chr12:104852800-104857400	Weak transcription	Psoas Muscle	Psoas
15	chr12:104853000-104854200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:104853000-104854200	Active TSS	Fetal Brain Female	brain
17	chr12:104853000-104854400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr12:104853000-104854800	Weak transcription	Liver	Liver
19	chr12:104853000-104855400	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr12:104853000-104855400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr12:104853000-104855600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:104853200-104854200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:104853200-104854400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:104853200-104854800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:104853200-104854800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:104853200-104854800	Weak transcription	Right Ventricle	heart
27	chr12:104853200-104855000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:104853200-104855400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:104853200-104855600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:104853200-104855600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr12:104853200-104856600	Weak transcription	Left Ventricle	heart
32	chr12:104853200-104868600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:104853400-104854200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr12:104853400-104854200	Enhancers	NHEK	skin
35	chr12:104853400-104854600	Weak transcription	Adipose Nuclei	Adipose
36	chr12:104853400-104854600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:104853400-104854600	Enhancers	Small Intestine	intestine
38	chr12:104853400-104854800	Enhancers	Colon Smooth Muscle	Colon
39	chr12:104853400-104854800	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:104853400-104855000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:104853400-104855000	Weak transcription	Placenta	Placenta
42	chr12:104853400-104855200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:104853400-104855400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:104853400-104855400	Enhancers	Brain Germinal Matrix	brain
45	chr12:104853400-104855400	Enhancers	Fetal Brain Male	brain
46	chr12:104853400-104856600	Weak transcription	Brain Substantia Nigra	brain
47	chr12:104853400-104862200	Weak transcription	Gastric	stomach
48	chr12:104853400-104863000	Weak transcription	Pancreas	Pancrea
49	chr12:104853400-104863200	Weak transcription	Aorta	Aorta
50	chr12:104853600-104854200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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