Variant report

Variant	rs12328613
Chromosome Location	chr2:20097874-20097875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20097277-20099218	K562	blood:	n/a	n/a
2	EBF1	chr2:20097827-20097989	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20068233..20072834-chr2:20097586..20102817,5	K562	blood:
2	chr2:20097107..20100415-chr2:20424161..20425989,3	K562	blood:

Variant related genes	Relation type
ENSG00000271991	TF binding region
ENSG00000115884	Chromatin interaction
ENSG00000228784	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10175236	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10175486	0.89[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10190645	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10203067	0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10211513	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11096633	0.88[CEU][hapmap];0.83[GIH][hapmap]
rs1147110	0.88[CEU][hapmap]
rs11887799	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12467740	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12478941	0.94[CEU][hapmap]
rs12615824	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1462754	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16987206	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16987297	0.94[CEU][hapmap]
rs2278528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28742930	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754907	0.87[CEU][hapmap]
rs3754908	0.87[CEU][hapmap]
rs3769763	0.87[CEU][hapmap]
rs58978345	0.84[AMR][1000 genomes]
rs6716854	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6717139	0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6721754	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6757734	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[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	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12328613	TTC32	cis	cerebellum	SCAN
rs12328613	TTC32	cis	lymphoblastoid	seeQTL
rs12328613	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs12328613	LOC130502	cis	multi-tissue	Pritchard
rs12328613	TTC32	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20069000-20098200	Weak transcription	Right Atrium	heart
2	chr2:20076600-20098200	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:20076800-20098400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:20076800-20099800	Weak transcription	Fetal Intestine Large	intestine
5	chr2:20079200-20098600	Weak transcription	Fetal Intestine Small	intestine
6	chr2:20079800-20099000	Weak transcription	Thymus	Thymus
7	chr2:20086600-20099800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:20088000-20099600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:20088400-20098200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:20089600-20098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:20089800-20099800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:20090400-20098200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:20090600-20098200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:20090600-20098400	Weak transcription	Right Ventricle	heart
15	chr2:20091000-20098400	Weak transcription	HSMM	muscle
16	chr2:20092200-20098800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr2:20092600-20098200	Weak transcription	Spleen	Spleen
18	chr2:20092600-20099600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:20092600-20100400	Weak transcription	Lung	lung
20	chr2:20093000-20099800	Enhancers	Liver	Liver
21	chr2:20093800-20098000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:20094000-20099600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:20094200-20099600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:20094200-20099600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr2:20094200-20100000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:20094600-20100200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:20094800-20099600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr2:20095000-20099800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr2:20095200-20099800	Enhancers	Rectal Smooth Muscle	rectum
30	chr2:20095400-20099600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:20095600-20098400	Weak transcription	Placenta	Placenta
32	chr2:20095600-20099800	Weak transcription	HSMMtube	muscle
33	chr2:20095800-20099600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:20095800-20099800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:20096000-20098000	Enhancers	Primary T cells from cord blood	blood
36	chr2:20096000-20100000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:20096200-20100000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:20096600-20098200	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr2:20096600-20099600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:20096600-20099800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr2:20096800-20099800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:20096800-20099800	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr2:20097000-20099800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:20097000-20099800	Enhancers	Brain Hippocampus Middle	brain
45	chr2:20097000-20099800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr2:20097200-20098000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:20097200-20098200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:20097200-20098200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:20097200-20098200	Enhancers	Colon Smooth Muscle	Colon
50	chr2:20097200-20098200	Genic enhancers	A549	lung

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