Variant report

Variant	rs12329657
Chromosome Location	chr21:15918714-15918715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:182)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:182 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr21:15918450-15918885	GM12878	blood:	n/a	n/a
2	TAF1	chr21:15918408-15918889	K562	blood:	n/a	n/a
3	POLR2A	chr21:15918144-15918900	GM12891	blood:	n/a	n/a
4	CREB1	chr21:15918276-15918926	K562	blood:	n/a	n/a
5	POLR2A	chr21:15918420-15918829	HL-60	blood:	n/a	n/a
6	SPI1	chr21:15918275-15918950	GM12878	blood:	n/a	chr21:15918700-15918713
7	SPI1	chr21:15918496-15918817	GM12891	blood:	n/a	chr21:15918700-15918713
8	ATF2	chr21:15918292-15918991	GM12878	blood:	n/a	n/a
9	MXI1	chr21:15917575-15918915	K562	blood:	n/a	n/a
10	MAFF	chr21:15918421-15918837	K562	blood:	n/a	n/a
11	POLR2A	chr21:15918375-15918776	GM12891	blood:	n/a	n/a
12	STAT3	chr21:15918589-15918885	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr21:15918489-15918781	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr21:15918290-15918881	GM12878	blood:	n/a	n/a
15	POLR2A	chr21:15918327-15918855	K562	blood:	n/a	n/a
16	STAT3	chr21:15918473-15918860	GM12878	blood:	n/a	n/a
17	POLR2A	chr21:15918336-15918856	GM12892	blood:	n/a	n/a
18	GTF2B	chr21:15918525-15918797	K562	blood:	n/a	n/a
19	ARID3A	chr21:15918034-15918949	K562	blood:	n/a	n/a
20	SIN3AK20	chr21:15918528-15918769	PFSK-1	brain:	n/a	n/a
21	MYC	chr21:15918232-15918885	K562	blood:	n/a	n/a
22	ATF1	chr21:15918475-15918878	K562	blood:	n/a	n/a
23	POLR2A	chr21:15918334-15918885	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr21:15918284-15918884	GM12891	blood:	n/a	n/a
25	POLR2A	chr21:15918315-15918793	GM12878	blood:	n/a	n/a
26	REST	chr21:15918539-15918719	GM12878	blood:	n/a	n/a
27	POLR2A	chr21:15918005-15918826	GM12878	blood:	n/a	n/a
28	KAP1	chr21:15918158-15918870	K562	blood:	n/a	n/a
29	USF1	chr21:15918532-15918742	K562	blood:	n/a	n/a
30	POLR2A	chr21:15918363-15918847	GM12878	blood:	n/a	n/a
31	ATF3	chr21:15918358-15918889	K562	blood:	n/a	n/a
32	MYC	chr21:15917803-15918891	K562	blood:	n/a	n/a
33	POLR2A	chr21:15918423-15918822	NB4	blood:	n/a	n/a
34	JUN	chr21:15918458-15918901	HUVEC	blood vessel:	n/a	chr21:15918875-15918884
35	RAD21	chr21:15918527-15918771	GM12878	blood:	n/a	n/a
36	POLR2A	chr21:15918418-15918846	GM12878	blood:	n/a	n/a
37	SPI1	chr21:15918384-15918993	HL-60	blood:	n/a	chr21:15918700-15918713
38	RUNX3	chr21:15918433-15918862	GM12878	blood:	n/a	n/a
39	FOS	chr21:15918624-15918825	MCF10A-Er-Src	breast:	n/a	n/a
40	NFIC	chr21:15918320-15918952	GM12878	blood:	n/a	n/a
41	EBF1	chr21:15918426-15918854	GM12878	blood:	n/a	n/a
42	FOXM1	chr21:15918359-15918924	GM12878	blood:	n/a	n/a
43	POLR2A	chr21:15917711-15918858	GM18505	blood:	n/a	n/a
44	CEBPD	chr21:15918409-15918910	K562	blood:	n/a	n/a
45	FOS	chr21:15918436-15918883	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr21:15918218-15918878	GM12892	blood:	n/a	n/a
47	GATA2	chr21:15918203-15918944	HUVEC	blood vessel:	n/a	chr21:15918675-15918682 chr21:15918672-15918686 chr21:15918673-15918682
48	TAF1	chr21:15918512-15918748	GM12892	blood:	n/a	n/a
49	CTCF	chr21:15918647-15918731	Spleen_OC	spleen:	n/a	n/a
50	POLR2A	chr21:15918239-15918841	GM12892	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:15916860..15919721-chr21:16123639..16127207,4	K562	blood:
2	chr21:15916876..15918776-chr21:16125268..16127207,2	K562	blood:
3	chr21:15918667..15923010-chr21:15942455..15946099,5	K562	blood:
4	chr21:15916155..15921451-chr21:15952417..15958327,11	K562	blood:

No data

Variant related genes	Relation type
SAMSN1	TF binding region
ENSG00000223662	Chromatin interaction
ENSG00000155307	Chromatin interaction
ENSG00000232884	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10854319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11702574	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11909106	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1882916	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1882917	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1974155	0.82[CHB][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs1980955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1985538	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2064024	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2178933	0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2178934	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2205366	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs2223092	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822754	0.80[TSI][hapmap]
rs2822760	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822761	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822762	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822763	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822765	0.94[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822767	0.89[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822776	0.81[CHB][hapmap];0.84[JPT][hapmap];0.80[TSI][hapmap]
rs2822777	0.81[CHB][hapmap];0.84[JPT][hapmap];0.80[TSI][hapmap]
rs3810580	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3930263	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs4817247	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4817248	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6516875	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6516876	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7275507	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7280293	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7282042	0.82[CHB][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap]
rs7510551	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8132641	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9980395	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9980490	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9981275	0.90[ASN][1000 genomes]
rs9983245	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059591	chr21:15835325-15969195	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1056423	chr21:15838309-15948474	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv544376	chr21:15855470-15948474	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1065823	chr21:15863224-15948474	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057934	chr21:15863224-15969195	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1058533	chr21:15896056-15948474	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv544377	chr21:15896056-15948474	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv834045	chr21:15900678-16112850	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv834046	chr21:15903792-16077369	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv2763685	chr21:15904945-15933282	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv587048	chr21:15908642-15932610	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv522627	chr21:15908642-15936503	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12329657	SAMSN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15913600-15919200	Active TSS	K562	blood
2	chr21:15914000-15918800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr21:15914000-15919000	Active TSS	GM12878-XiMat	blood
4	chr21:15914200-15918800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr21:15915600-15918800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr21:15916400-15918800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr21:15916600-15918800	Active TSS	Primary hematopoietic stem cells	blood
8	chr21:15916600-15918800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr21:15916600-15918800	Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr21:15916800-15918800	Active TSS	Primary monocytes fromperipheralblood	blood
11	chr21:15916800-15918800	Active TSS	Primary T cells fromperipheralblood	blood
12	chr21:15916800-15918800	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr21:15916800-15918800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr21:15916800-15919000	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr21:15917000-15918800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr21:15917000-15918800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr21:15917400-15918800	Active TSS	Fetal Thymus	thymus
18	chr21:15917400-15919000	Flanking Active TSS	HUVEC	blood vessel
19	chr21:15917600-15918800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr21:15917800-15918800	Active TSS	Primary B cells from peripheral blood	blood
21	chr21:15917800-15918800	Active TSS	Thymus	Thymus
22	chr21:15918000-15918800	Active TSS	Primary T cells from cord blood	blood
23	chr21:15918200-15918800	Active TSS	Placenta	Placenta
24	chr21:15918600-15918800	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr21:15918600-15918800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr21:15918600-15918800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr21:15918600-15918800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr21:15918600-15918800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr21:15918600-15918800	Flanking Active TSS	Dnd41	blood
30	chr21:15918600-15919000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr21:15918600-15919200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr21:15918600-15919400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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