Variant report

Variant	rs990211
Chromosome Location	chr3:48721040-48721041
allele	A/G
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	EP300	chr3:48720689-48721051	SK-N-SH_RA	brain:	n/a	chr3:48720833-48720842
2	MAFK	chr3:48720732-48721061	IMR90	lung:	n/a	n/a
3	NFIC	chr3:48720596-48721073	ECC-1	luminal epithelium:	n/a	chr3:48720803-48720819 chr3:48720803-48720820
4	ZNF263	chr3:48720766-48721121	HEK293-T-REx	kidney:	n/a	n/a
5	POLR2A	chr3:48720983-48721712	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:48720645-48721084	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr3:48720596-48721166	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr3:48720528-48721147	SK-N-SH	brain:	n/a	chr3:48720803-48720819 chr3:48720803-48720820
9	TCF12	chr3:48720489-48721223	SK-N-SH	brain:	n/a	chr3:48721136-48721144 chr3:48720551-48720559
10	NFIC	chr3:48720435-48721241	SK-N-SH	brain:	n/a	chr3:48720803-48720819 chr3:48720803-48720820

No.	Distal block	Cell Line	Cell type
1	chr3:48720285..48722202-chr3:49057646..49059671,2	MCF-7	breast:
2	chr3:48699573..48703813-chr3:48719476..48724654,10	MCF-7	breast:
3	chr3:48504852..48507133-chr3:48720810..48722542,3	MCF-7	breast:
4	chr3:48699299..48703873-chr3:48715927..48726939,20	MCF-7	breast:
5	chr3:48720679..48723641-chr3:49054826..49057455,2	K562	blood:
6	chr3:48720189..48722244-chr3:48955560..48957238,2	MCF-7	breast:
7	chr3:48670681..48672886-chr3:48719551..48721875,2	K562	blood:
8	chr3:48720909..48723341-chr3:49022618..49025566,2	K562	blood:
9	chr3:48720678..48725638-chr3:48726169..48732697,10	MCF-7	breast:
10	chr3:48715482..48719053-chr3:48720694..48722773,4	K562	blood:
11	chr3:48713537..48717616-chr3:48720627..48724588,5	MCF-7	breast:

Variant related genes	Relation type
NCKIPSD	TF binding region
ENSG00000213689	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000221883	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000273211	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000199032	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10865953	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs12632533	0.82[CEU][hapmap];1.00[GIH][hapmap]
rs14018	0.82[CEU][hapmap]
rs4858799	0.82[AMR][1000 genomes]
rs4858800	0.82[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap]
rs4858830	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4974088	0.82[CEU][hapmap]
rs6442129	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6766238	0.82[CEU][hapmap]
rs6796790	0.82[CEU][hapmap]
rs6806356	0.82[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7610519	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9284885	0.82[CEU][hapmap]
rs9311431	0.81[CEU][hapmap]
rs9822485	0.92[YRI][hapmap]
rs9859473	0.82[CEU][hapmap]
rs9874010	0.92[YRI][hapmap]
rs9879978	0.81[CEU][hapmap]
rs9882443	0.82[CEU][hapmap];1.00[GIH][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv590248	chr3:48716993-48727636	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs990211	AMT	cis	cerebellum	SCAN
rs990211	DALRD3	cis	parietal	SCAN
rs990211	PHF7	cis	parietal	SCAN
rs990211	QARS	cis	parietal	SCAN
rs990211	WDR6	cis	cerebellum	SCAN
rs990211	WDR6	cis	parietal	SCAN
rs990211	ZNF589	cis	parietal	SCAN
rs990211	P4HTM	cis	parietal	SCAN
rs990211	GMPPB	cis	parietal	SCAN
rs990211	NCKIPSD	cis	Muscle Skeletal	GTEx
rs990211	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs990211	WDR6	cis	Muscle Skeletal	GTEx
rs990211	QRICH1	cis	cerebellum	SCAN
rs990211	NICN1-AS1	cis	Thyroid	GTEx
rs990211	TLR9	cis	parietal	SCAN
rs990211	AMT	cis	Thyroid	GTEx
rs990211	DALRD3	cis	cerebellum	SCAN
rs990211	PBRM1	cis	parietal	SCAN
rs990211	NME6	cis	cerebellum	SCAN
rs990211	AMT	cis	Artery Tibial	GTEx
rs990211	AMT	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48701800-48721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:48702000-48721400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:48707200-48721400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:48709000-48721600	Weak transcription	Psoas Muscle	Psoas
5	chr3:48710400-48721200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:48711400-48721200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:48714600-48721200	Weak transcription	Small Intestine	intestine
8	chr3:48717400-48721200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:48717400-48721400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:48717800-48721800	Weak transcription	Primary B cells from cord blood	blood
11	chr3:48718200-48721600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:48718800-48721200	Weak transcription	HSMMtube	muscle
13	chr3:48718800-48725600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:48719000-48721200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:48719000-48722000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:48719000-48722000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:48719000-48722200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:48719600-48721400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:48719600-48722800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:48720000-48721200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:48720000-48721200	Weak transcription	Brain Substantia Nigra	brain
22	chr3:48720000-48721400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:48720000-48721600	Weak transcription	Primary T cells from cord blood	blood
24	chr3:48720000-48721600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:48720000-48721800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:48720000-48721800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:48720000-48722000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:48720200-48721200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:48720200-48721400	Weak transcription	Thymus	Thymus
30	chr3:48720200-48721600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:48720400-48721400	Enhancers	Ovary	ovary
32	chr3:48720400-48721600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:48720400-48721600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:48720400-48721600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:48720400-48721600	Enhancers	Liver	Liver
36	chr3:48720400-48721600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr3:48720400-48722000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:48720400-48722200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:48720400-48722200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:48720600-48721200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:48720600-48721200	Genic enhancers	Osteobl	bone
42	chr3:48720600-48721400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:48720600-48721400	Enhancers	Duodenum Mucosa	Duodenum
44	chr3:48720600-48721400	Genic enhancers	Fetal Intestine Large	intestine
45	chr3:48720600-48721400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr3:48720600-48721600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:48720600-48721600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:48720600-48721600	Enhancers	Colon Smooth Muscle	Colon
49	chr3:48720600-48721600	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr3:48720600-48721600	Enhancers	Rectal Mucosa Donor 29	rectum

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