Variant report

Variant	rs1072755
Chromosome Location	chr3:45975983-45975984
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	chr3:45973841..45976554-chr3:45977102..45979618,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11130080	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs12495073	0.92[CEU][hapmap]
rs12630101	1.00[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12635494	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12635657	1.00[CEU][hapmap]
rs12639598	0.96[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs13066048	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13073861	0.84[CEU][hapmap]
rs13091821	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13091979	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1532071	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1552489	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1552490	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1601867	0.92[ASN][1000 genomes]
rs17078449	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs1994488	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1994489	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1994490	0.81[CHD][hapmap];0.85[MEX][hapmap];0.80[ASN][1000 genomes]
rs2054866	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2131091	0.84[CEU][hapmap]
rs2171530	0.88[ASN][1000 genomes]
rs2234358	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.91[ASN][1000 genomes]
rs2248228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291470	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2373154	0.92[CEU][hapmap]
rs35465473	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3733100	0.80[ASN][1000 genomes]
rs3733103	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3774634	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3774635	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3774638	0.82[CHB][hapmap]
rs3774639	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796373	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[ASN][1000 genomes]
rs3796375	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821884	0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs4535265	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682799	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4682800	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4683147	0.82[CEU][hapmap]
rs4683148	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683149	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683152	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683153	0.81[ASN][1000 genomes]
rs4683154	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683156	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683157	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60779624	0.81[ASN][1000 genomes]
rs62245108	0.81[ASN][1000 genomes]
rs6778225	0.81[ASN][1000 genomes]
rs6778324	0.81[ASN][1000 genomes]
rs6778896	0.82[EUR][1000 genomes]
rs6781121	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs6800954	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs7129	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs730983	0.96[CEU][hapmap]
rs737452	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs751552	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs751553	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9311380	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs936938	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs936939	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs9824253	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9831315	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1072755	CXCR6	cis	parietal	SCAN
rs1072755	UBA7	cis	parietal	SCAN
rs1072755	SS18L2	cis	parietal	SCAN
rs1072755	DALRD3	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:45958800-45980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:45958800-45980200	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
5	chr3:45959200-45979800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:45959200-45980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:45959800-45979800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:45959800-45979800	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:45959800-45980400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:45960000-45979400	Strong transcription	Fetal Intestine Large	intestine
12	chr3:45960000-45980400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:45960400-45980200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:45961600-45979400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:45961600-45979800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:45963200-45985200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:45963800-45979800	Strong transcription	Primary T cells from cord blood	blood
18	chr3:45963800-45979800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:45964400-45980400	Weak transcription	Fetal Brain Female	brain
20	chr3:45965400-45977600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:45965400-45980400	Weak transcription	Fetal Brain Male	brain
22	chr3:45966000-45980600	Weak transcription	HMEC	breast
23	chr3:45966800-45979600	Strong transcription	Liver	Liver
24	chr3:45967000-45976600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:45967000-45978200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr3:45967200-45977600	Strong transcription	Primary B cells from cord blood	blood
27	chr3:45967200-45979400	Strong transcription	Adipose Nuclei	Adipose
28	chr3:45967200-45979800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:45967200-45980000	Strong transcription	Fetal Muscle Leg	muscle
30	chr3:45967400-45979800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:45967800-45976200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:45968000-45979200	Strong transcription	Placenta	Placenta
33	chr3:45968400-45979800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr3:45968400-45979800	Strong transcription	Ovary	ovary
35	chr3:45968600-45978800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:45968600-45979000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:45968600-45979800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr3:45968600-45980200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:45968800-45976000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:45968800-45979200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:45968800-45979200	Strong transcription	HepG2	liver
42	chr3:45968800-45979400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:45968800-45979400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:45968800-45979400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:45969000-45977400	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr3:45969000-45978400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:45969000-45978600	Strong transcription	K562	blood
48	chr3:45969000-45979000	Strong transcription	Brain Substantia Nigra	brain
49	chr3:45969000-45979200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:45969000-45979200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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