Variant report

Variant	rs9887974
Chromosome Location	chr1:193279932-193279933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:193277193..193280125-chr1:193280849..193282913,2	MCF-7	breast:
2	chr1:193278831..193281836-chr1:193282854..193285758,3	K562	blood:

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10494674	0.86[CHB][hapmap]
rs10732293	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes]
rs10733078	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs10737621	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs10737622	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10737623	0.80[ASN][1000 genomes]
rs10754044	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10754047	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10754048	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10754049	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs10754052	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs10754055	0.80[ASN][1000 genomes]
rs10801177	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs10801178	0.87[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap]
rs10801179	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs10801183	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10801184	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs10801187	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs10801188	0.80[EUR][1000 genomes]
rs10801189	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs10801190	0.89[EUR][1000 genomes]
rs10801191	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10801192	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10801194	0.97[ASN][1000 genomes]
rs10921318	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10921323	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs10921325	0.82[GIH][hapmap]
rs10921326	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs10921328	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10921330	0.87[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs10921334	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11577299	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs12064521	0.87[EUR][1000 genomes]
rs12078145	0.93[EUR][1000 genomes]
rs12090626	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap]
rs12124282	0.93[EUR][1000 genomes]
rs12126529	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs12145057	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs1221502	1.00[ASN][1000 genomes]
rs12410213	0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs1325197	0.95[CHB][hapmap];0.82[GIH][hapmap]
rs1361404	0.92[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1408830	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes]
rs1416977	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1536098	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1536099	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs1539724	0.87[CEU][hapmap];0.92[GIH][hapmap];0.80[LWK][hapmap];0.97[TSI][hapmap]
rs1578242	0.92[EUR][1000 genomes]
rs1578243	0.92[EUR][1000 genomes]
rs1616234	0.97[ASN][1000 genomes]
rs1632444	0.80[ASN][1000 genomes]
rs1770000	0.94[EUR][1000 genomes]
rs1972344	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1972345	0.98[ASN][1000 genomes]
rs2182106	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs2186016	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs2251699	0.87[EUR][1000 genomes]
rs2254646	0.80[ASN][1000 genomes]
rs2370029	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs2370264	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477549	0.98[ASN][1000 genomes]
rs2486843	0.94[EUR][1000 genomes]
rs3738244	0.87[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs3806351	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs4379660	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs4450000	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap]
rs4466634	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap]
rs4657744	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap]
rs4657747	0.82[EUR][1000 genomes]
rs4657847	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs4657848	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs474328	0.86[EUR][1000 genomes]
rs503265	0.80[ASN][1000 genomes]
rs523402	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531327	0.93[EUR][1000 genomes]
rs543788	0.80[ASN][1000 genomes]
rs560900	0.98[ASN][1000 genomes]
rs569656	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs571029	0.80[ASN][1000 genomes]
rs578639	1.00[ASN][1000 genomes]
rs6428152	0.95[CHB][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs6428154	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs6428156	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs6428157	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6428159	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs6662104	0.88[EUR][1000 genomes]
rs6665069	0.95[CHB][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs6665666	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs6671237	0.95[CHB][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs6671476	0.80[ASN][1000 genomes]
rs6673271	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs6675827	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6675833	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs6676878	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs6680224	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs6689006	0.87[EUR][1000 genomes]
rs6697079	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs6702762	0.88[EUR][1000 genomes]
rs693519	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7514072	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs7515024	0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs7518792	0.95[CHB][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs7519242	0.95[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs7534504	0.83[EUR][1000 genomes]
rs7543029	0.88[EUR][1000 genomes]
rs817138	0.99[ASN][1000 genomes]
rs817140	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs817142	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs817143	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs843844	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.99[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	nsv832148	chr1:193143945-193292897	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv872831	chr1:193152317-193322087	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1001174	chr1:193186758-193363372	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv997891	chr1:193271839-193566441	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9887974	CDC73	cis	cerebellum	SCAN
rs9887974	GLRX2	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193255200-193280400	Weak transcription	HSMM	muscle
2	chr1:193276600-193283400	Enhancers	Fetal Intestine Small	intestine
3	chr1:193277000-193283400	Enhancers	Fetal Intestine Large	intestine
4	chr1:193278600-193280600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr1:193278800-193280400	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr1:193279000-193281200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:193279200-193280600	Enhancers	Primary T cells from cord blood	blood
8	chr1:193279200-193281200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:193279400-193280000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:193279400-193280200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:193279400-193280200	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr1:193279400-193280600	Enhancers	Fetal Thymus	thymus
13	chr1:193279400-193281000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:193279400-193281000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:193279400-193281000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:193279600-193280000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:193279600-193280200	Enhancers	Thymus	Thymus
18	chr1:193279600-193280400	Enhancers	HepG2	liver
19	chr1:193279600-193280800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr1:193279600-193281000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:193279600-193282800	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:193279800-193280000	Enhancers	Fetal Brain Male	brain

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