Variant report

Variant	rs2107538
Chromosome Location	chr17:34207780-34207781
allele	C/T
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	JUN	chr17:34207734-34207908	K562	blood:	n/a	n/a
2	WRNIP1	chr17:34206877-34208188	GM12878	blood:	n/a	n/a
3	ATF1	chr17:34207694-34208304	K562	blood:	n/a	n/a
4	MTA3	chr17:34206649-34207913	GM12878	blood:	n/a	n/a
5	EP300	chr17:34207197-34207781	GM12878	blood:	n/a	chr17:34207484-34207498 chr17:34207477-34207491
6	RELA	chr17:34206888-34208027	GM12878	blood:	n/a	n/a
7	RELA	chr17:34206846-34207781	GM10847	blood:	n/a	n/a
8	RUNX3	chr17:34207028-34207799	GM12878	blood:	n/a	n/a
9	CEBPB	chr17:34206667-34207902	GM12878	blood:	n/a	n/a
10	NFIC	chr17:34206674-34208045	GM12878	blood:	n/a	n/a
11	ATF2	chr17:34207025-34207889	GM12878	blood:	n/a	n/a
12	GATA2	chr17:34207545-34207970	HUVEC	blood vessel:	n/a	n/a
13	MTA3	chr17:34206727-34207941	GM12878	blood:	n/a	n/a
14	RELA	chr17:34206894-34207995	GM18505	blood:	n/a	n/a
15	NFIC	chr17:34207110-34207849	GM12878	blood:	n/a	n/a
16	RELA	chr17:34206827-34207801	GM12891	blood:	n/a	n/a
17	BCL3	chr17:34207131-34207861	GM12878	blood:	n/a	n/a
18	STAT5A	chr17:34206770-34208014	GM12878	blood:	n/a	chr17:34206865-34206879 chr17:34207470-34207478 chr17:34207319-34207331
19	MXI1	chr17:34206988-34207791	GM12878	blood:	n/a	n/a
20	PML	chr17:34206629-34207793	GM12878	blood:	n/a	n/a
21	RELA	chr17:34206946-34207937	GM18951	blood:	n/a	n/a
22	POLR2A	chr17:34206835-34207847	GM12891	blood:	n/a	n/a
23	NFATC1	chr17:34206870-34207790	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CCL5	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11650668	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11653282	0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs11868244	0.92[ASN][1000 genomes]
rs11868785	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs1994182	0.83[CEU][hapmap]
rs2251660	0.92[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2280787	0.86[EUR][1000 genomes]
rs2280789	0.80[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2291299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306630	0.80[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2376287	0.86[EUR][1000 genomes]
rs2526327	0.92[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2526328	0.85[EUR][1000 genomes]
rs2702947	0.83[EUR][1000 genomes]
rs2702948	0.83[EUR][1000 genomes]
rs2735475	0.92[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs28595279	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28722787	0.86[EUR][1000 genomes]
rs34369685	0.83[EUR][1000 genomes]
rs3760327	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3817655	1.00[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826404	0.83[CEU][hapmap];0.80[CHB][hapmap];0.85[TSI][hapmap]
rs4079183	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4239252	0.86[EUR][1000 genomes]
rs4251703	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4251710	0.92[LWK][hapmap];0.86[MKK][hapmap];0.81[YRI][hapmap]
rs4251719	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4251724	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs4251737	0.85[ASN][1000 genomes]
rs4251749	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4251769	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4251787	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4251791	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4325615	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4795087	0.83[CHB][hapmap]
rs4795090	0.89[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap]
rs4795093	0.88[ASN][1000 genomes]
rs4795096	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4795101	0.85[EUR][1000 genomes]
rs4796105	0.91[CEU][hapmap];0.84[TSI][hapmap]
rs4796116	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796123	0.80[CEU][hapmap]
rs4796128	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4796133	0.86[EUR][1000 genomes]
rs4796134	0.86[EUR][1000 genomes]
rs4796136	0.86[EUR][1000 genomes]
rs4796137	0.86[EUR][1000 genomes]
rs4796138	0.92[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs55950249	0.90[ASN][1000 genomes]
rs6505496	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap]
rs6505498	0.81[AFR][1000 genomes]
rs7211393	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213636	0.86[EUR][1000 genomes]
rs7215845	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8066406	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8069014	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8080959	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9303692	0.80[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9754	0.92[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs9889874	0.80[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9890583	0.86[EUR][1000 genomes]
rs9899881	0.86[EUR][1000 genomes]
rs9900236	0.85[MEX][hapmap]
rs9900563	0.91[ASN][1000 genomes]
rs9908928	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9909416	0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs9913559	0.87[GIH][hapmap];0.86[EUR][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2107538	AMAC1	cis	cerebellum	SCAN
rs2107538	CCL5	cis	lymphoblastoid	seeQTL
rs2107538	RDM1	cis	lymphoblastoid	seeQTL
rs2107538	RDM1	cis	parietal	SCAN
rs2107538	RDM1	cis	multi-tissue	Pritchard
rs2107538	TAF15	cis	normal skin	skin_eQTL
rs2107538	C17orf50	cis	cerebellum	SCAN
rs2107538	TAF15	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34192200-34218000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr17:34192400-34213200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:34202600-34207800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr17:34203800-34207800	Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr17:34205600-34207800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
6	chr17:34206800-34207800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:34206800-34208000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr17:34206800-34208000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr17:34206800-34208000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:34206800-34208000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr17:34206800-34208000	Enhancers	Placenta	Placenta
12	chr17:34206800-34208000	Flanking Active TSS	GM12878-XiMat	blood
13	chr17:34207000-34207800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr17:34207000-34207800	Enhancers	Fetal Thymus	thymus
15	chr17:34207000-34208000	Enhancers	HUVEC	blood vessel
16	chr17:34207200-34207800	Enhancers	Fetal Muscle Leg	muscle
17	chr17:34207400-34219200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:34207600-34207800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr17:34207600-34207800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:34207600-34207800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr17:34207600-34208000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr17:34207600-34208000	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr17:34207600-34208000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr17:34207600-34208000	Flanking Active TSS	K562	blood
25	chr17:34207600-34208200	Enhancers	Primary B cells from peripheral blood	blood
26	chr17:34207600-34208200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr17:34207600-34208400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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