Variant report

Variant	rs10486549
Chromosome Location	chr7:27672895-27672896
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	chr7:27667898..27670542-chr7:27670905..27674481,3	MCF-7	breast:
2	chr7:27671208..27672985-chr7:27680349..27682159,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10267854	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[LWK][hapmap];0.89[TSI][hapmap]
rs10486559	0.91[CEU][hapmap]
rs11550134	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12666082	0.81[EUR][1000 genomes]
rs12667470	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12670250	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs12671723	0.91[JPT][hapmap]
rs12700831	0.83[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs1524525	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1524527	0.86[JPT][hapmap]
rs17150563	0.82[EUR][1000 genomes]
rs17155443	0.85[JPT][hapmap]
rs17155498	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17155501	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17155505	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17155525	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17155537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17155702	0.82[ASW][hapmap];0.91[CEU][hapmap]
rs2074579	0.90[CEU][hapmap]
rs2074769	0.91[CEU][hapmap]
rs2108309	0.89[CEU][hapmap]
rs2192559	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2391450	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2893292	0.86[JPT][hapmap]
rs3779473	0.83[CEU][hapmap]
rs42089	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs42100	0.84[JPT][hapmap]
rs4719908	0.86[CEU][hapmap]
rs58231871	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58857361	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59686784	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61407744	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62454870	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62454871	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62454872	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62454876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62454908	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62454914	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62456947	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62456951	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6944251	0.91[CEU][hapmap]
rs6947004	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6975900	0.81[JPT][hapmap]
rs72596952	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72596966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs759268	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs759272	0.91[JPT][hapmap]
rs7778454	0.90[JPT][hapmap]
rs7784038	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[LWK][hapmap];0.89[TSI][hapmap]
rs7803227	0.86[CEU][hapmap]
rs7809735	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv1802647	chr7:27658495-27673924	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10486549	CRHR2	cis	parietal	SCAN
rs10486549	SCRN1	cis	cerebellum	SCAN
rs10486549	HOXA13	cis	parietal	SCAN
rs10486549	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10486549	PRR15	cis	parietal	SCAN
rs10486549	HOXA9	cis	parietal	SCAN
rs10486549	TRIL	cis	parietal	SCAN
rs10486549	SNX10	cis	cerebellum	SCAN
rs10486549	HIBADH	cis	parietal	SCAN
rs10486549	ACSL6	trans	parietal	SCAN
rs10486549	TAX1BP1	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27651800-27674200	Weak transcription	Hela-S3	cervix
2	chr7:27654400-27696400	Weak transcription	Gastric	stomach
3	chr7:27658800-27687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:27658800-27688600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:27659800-27675400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr7:27659800-27679000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:27660000-27680600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:27660200-27674600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:27660400-27675600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:27660400-27680200	Weak transcription	Fetal Kidney	kidney
11	chr7:27660600-27674800	Weak transcription	Psoas Muscle	Psoas
12	chr7:27660600-27701000	Weak transcription	Right Ventricle	heart
13	chr7:27660800-27675600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:27660800-27676400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:27661000-27675000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:27661000-27675400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:27661000-27679600	Weak transcription	HSMMtube	muscle
18	chr7:27661000-27680600	Weak transcription	HepG2	liver
19	chr7:27661000-27688000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr7:27661200-27675200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:27661200-27694800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr7:27661400-27675200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:27661400-27688800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:27661400-27700800	Weak transcription	Thymus	Thymus
25	chr7:27661600-27681000	Weak transcription	NHEK	skin
26	chr7:27661800-27674400	Weak transcription	Aorta	Aorta
27	chr7:27661800-27675800	Weak transcription	Primary B cells from cord blood	blood
28	chr7:27661800-27680200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr7:27661800-27681400	Weak transcription	Pancreas	Pancrea
30	chr7:27661800-27686400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:27661800-27692200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:27661800-27694400	Weak transcription	Lung	lung
33	chr7:27662000-27675200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr7:27662200-27674400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:27662400-27686800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:27662600-27688200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:27662800-27674200	Weak transcription	Brain Substantia Nigra	brain
38	chr7:27662800-27688000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr7:27663000-27674400	Weak transcription	Brain Angular Gyrus	brain
40	chr7:27663200-27674400	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:27663200-27675000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:27664000-27675200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr7:27664400-27680400	Weak transcription	NH-A	brain
44	chr7:27664600-27681400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:27664800-27688200	Weak transcription	K562	blood
46	chr7:27665000-27680400	Weak transcription	NHDF-Ad	bronchial
47	chr7:27665000-27681000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:27665000-27686000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:27665600-27680000	Weak transcription	HUVEC	blood vessel
50	chr7:27665800-27675200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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