Variant report

Variant	rs2633580
Chromosome Location	chr3:112219753-112219754
allele	C/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	POLR2A	chr3:112219489-112219823	HUVEC	blood vessel:	n/a	n/a
2	JUN	chr3:112219484-112219842	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:112219406-112219827	HUVEC	blood vessel:	n/a	n/a
4	GATA2	chr3:112219451-112219941	HUVEC	blood vessel:	n/a	chr3:112219675-112219685
5	FOS	chr3:112219390-112219897	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:112219346-112219956	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:112219336-112220020	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112215809..112217939-chr3:112219323..112221326,2	K562	blood:

Variant related genes	Relation type
BTLA	TF binding region

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10755071	0.85[ASN][1000 genomes]
rs11706550	0.87[EUR][1000 genomes]
rs12632867	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs1386895	0.83[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1398091	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs1512005	0.87[EUR][1000 genomes]
rs1512006	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1533159	0.81[CHB][hapmap]
rs1844089	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873571	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs1873572	0.81[CHB][hapmap]
rs1877363	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1994713	0.87[EUR][1000 genomes]
rs2101632	0.80[ASN][1000 genomes]
rs2131008	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2171513	0.81[CHB][hapmap]
rs2279532	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2280066	0.87[EUR][1000 genomes]
rs2464611	0.88[ASN][1000 genomes]
rs2633555	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2633562	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs2633574	0.81[CHB][hapmap]
rs2633578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633579	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs2633582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633584	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2638017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2638018	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2638019	0.81[CHB][hapmap]
rs2638022	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2638023	0.81[CHB][hapmap]
rs2638026	0.81[CHB][hapmap]
rs2638029	0.81[CHB][hapmap]
rs2638031	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs2638032	0.81[CHB][hapmap]
rs2638035	0.81[CHB][hapmap]
rs2638037	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2638039	0.91[CHB][hapmap]
rs2638042	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2638045	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2668217	0.80[ASN][1000 genomes]
rs2668220	0.80[ASN][1000 genomes]
rs2668222	0.80[ASN][1000 genomes]
rs2705507	0.81[CHB][hapmap]
rs2705517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2705521	0.81[CHB][hapmap]
rs2705522	0.81[CHB][hapmap]
rs2705531	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2705532	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2705534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2705541	0.81[CHB][hapmap]
rs2705543	0.80[ASN][1000 genomes]
rs2705544	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs2705556	0.81[CHB][hapmap]
rs2705559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2705562	0.81[CHB][hapmap]
rs2705565	0.82[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs2705566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28866814	0.87[EUR][1000 genomes]
rs2933134	0.81[CHB][hapmap]
rs2933135	0.81[CHB][hapmap]
rs2933142	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2952319	0.81[CHB][hapmap]
rs2952323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2952327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2969895	0.80[CHB][hapmap]
rs2969896	0.81[CHB][hapmap]
rs2971204	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs34233684	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732815	0.87[EUR][1000 genomes]
rs4519670	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4682410	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4682413	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5000995	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6438079	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes]
rs6772077	0.82[ASN][1000 genomes]
rs6774355	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792947	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs728568	0.81[CHB][hapmap]
rs7625366	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7652377	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs766968	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9288952	0.88[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap]
rs9288954	0.87[EUR][1000 genomes]
rs9756562	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809247	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9848054	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9854043	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9866734	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9869455	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9869579	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2633580	SLC35A5	cis	multi-tissue	Pritchard
rs2633580	SLC35A5	cis	lymphoblastoid	seeQTL
rs2633580	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112214600-112228600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:112218400-112220000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:112218400-112220600	Enhancers	HUVEC	blood vessel
4	chr3:112218600-112222400	Weak transcription	Fetal Thymus	thymus
5	chr3:112218800-112219800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:112218800-112219800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:112218800-112220800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr3:112218800-112222800	Enhancers	Primary B cells from peripheral blood	blood
9	chr3:112218800-112241600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr3:112219000-112219800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:112219000-112219800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:112219000-112219800	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr3:112219000-112225000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:112219400-112221200	Enhancers	Primary T cells from cord blood	blood
15	chr3:112219400-112221200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:112219600-112219800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr3:112219600-112219800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr3:112219600-112219800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:112219600-112222200	Weak transcription	GM12878-XiMat	blood

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