Variant report

Variant	rs11682173
Chromosome Location	chr2:100759810-100759811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT5A	chr2:100758432-100759817	GM12878	blood:	n/a	chr2:100759445-100759456 chr2:100758535-100758546 chr2:100759632-100759639 chr2:100759420-100759431

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:100759810-100759860	GM12878	blood:	n/a
2	chr2:100759810-100759860	T-47D	breast:	n/a
3	chr2:100759810-100759860	HRE	kidney:	n/a
4	chr2:100759810-100759860	ECC-1	luminal epithelium:	n/a
5	chr2:100759810-100759860	HIPEpiC	eye:	n/a
6	chr2:100759810-100759860	HRCEpiC	kidney:	n/a
7	chr2:100759810-100759860	PrEC	prostate:	n/a
8	chr2:100759810-100759860	HMEC	breast:	n/a
9	chr2:100759810-100759860	SK-N-SH	brain:	n/a
10	chr2:100759810-100759860	HUVEC	blood vessel:	n/a
11	chr2:100759810-100759860	IMR90	lung:	fetal
12	chr2:100759810-100759860	LNCaP	prostate:	n/a
13	chr2:100759810-100759860	Hepatocyte	liver:	n/a
14	chr2:100759810-100759860	HRPEpiC	eye:	n/a
15	chr2:100759810-100759860	ovcar-3	ovarian:	n/a
16	chr2:100759810-100759860	AG09319	gingival:	n/a
17	chr2:100759810-100759860	H1-hESC	embryonic stem cell:	embryo
18	chr2:100759810-100759860	SK-N-MC	brain:	n/a
19	chr2:100759810-100759860	GM12891	blood:	n/a
20	chr2:100759810-100759860	MCF10A-Er-Src	breast:	n/a
21	chr2:100759810-100759860	HEEpiC	esophagus:	n/a
22	chr2:100759810-100759860	CMK	blood:	n/a
23	chr2:100759810-100759860	MCF-7	breast:	n/a
24	chr2:100759810-100759860	NHDF-neo	bronchial:	n/a
25	chr2:100759810-100759860	HL-60	blood:	n/a
26	chr2:100759810-100759860	NHBE	bronchial:	n/a
27	chr2:100759810-100759860	Caco-2	colon:	n/a
28	chr2:100759810-100759860	Jurkat	blood:	n/a
29	chr2:100759810-100759860	ProgFib	skin:	n/a
30	chr2:100759810-100759860	PFSK-1	brain:	n/a
31	chr2:100759810-100759860	SAEC	small airway:	n/a
32	chr2:100759810-100759860	GM12892	blood:	n/a
33	chr2:100759810-100759860	SKMC	muscle:	n/a
34	chr2:100759810-100759860	HAEpiC	amniotic membrane:	n/a
35	chr2:100759810-100759860	AoSMC	blood vessel:	n/a
36	chr2:100759810-100759860	AG04449	skin:	fetal
37	chr2:100759810-100759860	HNPCEpiC	eye:	n/a
38	chr2:100759810-100759860	AG09309	skin:	n/a
39	chr2:100759810-100759860	NH-A	brain:	n/a
40	chr2:100759810-100759860	PANC-1	pancreas:	n/a
41	chr2:100759810-100759860	U87	brain:	n/a
42	chr2:100759810-100759860	NT2-D1	testis:	n/a
43	chr2:100759810-100759860	GM19239	blood:	n/a
44	chr2:100759810-100759860	AG04450	lung:	fetal
45	chr2:100759810-100759860	A549	lung:	n/a
46	chr2:100759810-100759860	BE2_C	brain:	n/a
47	chr2:100759810-100759860	AG10803	skin:	n/a
48	chr2:100759810-100759860	HPAEpiC	pulmonary alveolar:	n/a
49	chr2:100759810-100759860	HCM	heart:	n/a
50	chr2:100759810-100759860	HCPEpiC	choroid plexus:	n/a

No data

Variant related genes	Relation type
AFF3	TF binding region
AFF3	CpG island

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11123808	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11123809	0.81[ASN][1000 genomes]
rs11123810	0.81[ASN][1000 genomes]
rs11123811	0.80[ASN][1000 genomes]
rs11123812	0.81[ASN][1000 genomes]
rs11677607	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11679078	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11680485	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11680586	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11681966	0.81[ASN][1000 genomes]
rs11686599	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11689956	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11690905	0.81[ASN][1000 genomes]
rs11691486	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11692215	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11900482	0.81[ASN][1000 genomes]
rs12712064	0.81[ASN][1000 genomes]
rs12712065	0.80[ASN][1000 genomes]
rs12712067	0.85[YRI][hapmap]
rs12712069	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12712072	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12987209	0.81[ASN][1000 genomes]
rs12987212	0.81[ASN][1000 genomes]
rs13000759	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13003982	0.81[ASN][1000 genomes]
rs13010436	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13011181	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13011874	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13019618	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13022707	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13028981	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13032454	0.81[ASN][1000 genomes]
rs3748927	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4850920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4850921	0.85[YRI][hapmap]
rs4851252	0.81[ASN][1000 genomes]
rs4851254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851262	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6713524	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7583067	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7596385	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv582530	chr2:100739970-100774287	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv527481	chr2:100753490-100763006	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11682173	MGAT4A	cis	parietal	SCAN
rs11682173	SNRNP200	cis	parietal	SCAN
rs11682173	AFF3	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100746200-100764800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:100758200-100761600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:100758800-100765600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:100759000-100763000	Weak transcription	Adipose Nuclei	Adipose
5	chr2:100759200-100760400	Enhancers	Fetal Thymus	thymus
6	chr2:100759200-100760600	Enhancers	Primary hematopoietic stem cells	blood
7	chr2:100759200-100760800	ZNF genes & repeats	GM12878-XiMat	blood
8	chr2:100759200-100761400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:100759200-100763400	Enhancers	Primary B cells from peripheral blood	blood
10	chr2:100759400-100760000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr2:100759400-100760000	Enhancers	Thymus	Thymus
12	chr2:100759400-100760200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:100759600-100760000	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr2:100759600-100761400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:100759800-100760000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr2:100759800-100760000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr2:100759800-100760400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:100759800-100761000	Weak transcription	Spleen	Spleen
19	chr2:100759800-100761400	Enhancers	Dnd41	blood
20	chr2:100759800-100762000	Enhancers	Primary B cells from cord blood	blood

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