Variant report

Variant	rs4769781
Chromosome Location	chr13:30512789-30512790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30512486..30516242-chr13:30529306..30532066,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1093631	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1325368	0.84[ASN][1000 genomes]
rs1359475	0.85[CEU][hapmap]
rs17631642	0.84[ASN][1000 genomes]
rs17688104	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs3843677	0.88[ASN][1000 genomes]
rs3843678	0.85[ASN][1000 genomes]
rs4318068	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4769779	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4769780	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585668	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634413	0.96[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs646917	0.80[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7319246	0.87[ASN][1000 genomes]
rs7320271	0.87[ASN][1000 genomes]
rs7320355	0.87[ASN][1000 genomes]
rs7320728	0.87[ASN][1000 genomes]
rs7322038	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7339208	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74042894	0.87[ASN][1000 genomes]
rs7992473	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs7994222	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs818608	0.81[TSI][hapmap]
rs843883	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912788	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs927731	0.84[ASN][1000 genomes]
rs927732	0.87[ASN][1000 genomes]
rs927733	0.82[ASN][1000 genomes]
rs9314990	0.85[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs9314991	0.85[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs9506244	0.85[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs9508594	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4769781	MTIF3	cis	parietal	SCAN
rs4769781	SH3BGRL2	trans	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30498800-30513200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:30509400-30512800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr13:30509800-30515000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr13:30510400-30515000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr13:30510600-30512800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr13:30510600-30512800	Enhancers	Thymus	Thymus
7	chr13:30510600-30513000	Enhancers	Fetal Thymus	thymus
8	chr13:30510800-30521600	Weak transcription	Pancreas	Pancrea
9	chr13:30511000-30513000	Enhancers	Primary T cells from cord blood	blood
10	chr13:30511000-30513000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr13:30511200-30513000	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr13:30511600-30513400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr13:30511600-30514000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr13:30511600-30514400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr13:30511600-30514800	Weak transcription	Liver	Liver
16	chr13:30511800-30514400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr13:30512000-30513200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:30512200-30514200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr13:30512400-30513000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
20	chr13:30512400-30513000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr13:30512400-30513200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:30512400-30513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr13:30512400-30514000	Enhancers	Primary T cells fromperipheralblood	blood
24	chr13:30512400-30514200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr13:30512400-30518400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr13:30512600-30513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr13:30512600-30513800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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