Variant report

Variant	rs3751322
Chromosome Location	chr12:104853787-104853788
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: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10778334	1.00[ASN][1000 genomes]
rs12299738	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1922261	0.93[LWK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs3751318	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs3751319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812797	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	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
rs3751322	CHST11	cis	cerebellar cortex	BrainEAC
rs3751322	CHST11	cis	cerebellum	SCAN
rs3751322	SPIC	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104850000-104853800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr12:104850200-104853800	Active TSS	Primary T killer memory cells from peripheral blood	blood
3	chr12:104850200-104854400	Active TSS	Thymus	Thymus
4	chr12:104850200-104854600	Active TSS	GM12878-XiMat	blood
5	chr12:104850400-104853800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr12:104850800-104855800	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr12:104852000-104855600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
8	chr12:104852200-104855400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr12:104852400-104854000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:104852400-104854200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr12:104852400-104855600	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr12:104852600-104853800	Active TSS	Brain Cingulate Gyrus	brain
13	chr12:104852600-104854200	Flanking Active TSS	Fetal Thymus	thymus
14	chr12:104852600-104854400	Active TSS	Colonic Mucosa	Colon
15	chr12:104852600-104854800	Flanking Active TSS	K562	blood
16	chr12:104852600-104855000	Active TSS	Brain Hippocampus Middle	brain
17	chr12:104852800-104854000	Weak transcription	Spleen	Spleen
18	chr12:104852800-104854200	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr12:104852800-104855000	Active TSS	Duodenum Mucosa	Duodenum
20	chr12:104852800-104857400	Weak transcription	Psoas Muscle	Psoas
21	chr12:104853000-104853800	Flanking Active TSS	HMEC	breast
22	chr12:104853000-104854000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:104853000-104854000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:104853000-104854200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:104853000-104854200	Active TSS	Fetal Brain Female	brain
26	chr12:104853000-104854400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr12:104853000-104854800	Weak transcription	Liver	Liver
28	chr12:104853000-104855400	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr12:104853000-104855400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr12:104853000-104855600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:104853200-104853800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr12:104853200-104854200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:104853200-104854400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:104853200-104854800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:104853200-104854800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:104853200-104854800	Weak transcription	Right Ventricle	heart
37	chr12:104853200-104855000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:104853200-104855400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:104853200-104855600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:104853200-104855600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr12:104853200-104856600	Weak transcription	Left Ventricle	heart
42	chr12:104853200-104868600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:104853400-104853800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:104853400-104853800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
45	chr12:104853400-104853800	Active TSS	Primary T cells fromperipheralblood	blood
46	chr12:104853400-104853800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:104853400-104853800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr12:104853400-104854000	Enhancers	H9 Cell Line	embryonic stem cell
49	chr12:104853400-104854000	Enhancers	Rectal Smooth Muscle	rectum
50	chr12:104853400-104854000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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