Variant report

Variant	rs3779522
Chromosome Location	chr7:127707175-127707176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127707069..127708386-chr7:127849479..127850121,3	MCF-7	breast:
2	chr7:127701353..127703236-chr7:127706938..127708859,2	K562	blood:
3	chr7:127705316..127708471-chr7:127714024..127716171,3	MCF-7	breast:
4	chr7:127703319..127705715-chr7:127706907..127711079,5	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1024910	0.90[AMR][1000 genomes]
rs11768841	0.82[AMR][1000 genomes]
rs1193331	0.82[AMR][1000 genomes]
rs1193333	0.86[AMR][1000 genomes]
rs1193335	0.88[AMR][1000 genomes]
rs124756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1345509	0.83[JPT][hapmap]
rs2241291	0.82[ASW][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs2543477	0.83[AMR][1000 genomes]
rs322781	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs322813	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs322816	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322817	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs322819	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322820	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322821	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs322823	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322825	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322826	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs322827	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs322828	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs322829	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs322830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs322832	0.98[ASN][1000 genomes]
rs322833	0.98[ASN][1000 genomes]
rs322837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs322840	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757753	0.99[ASN][1000 genomes]
rs3757754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757760	0.82[ASW][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs3757763	0.85[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.88[AMR][1000 genomes]
rs3757771	0.84[AMR][1000 genomes]
rs3779523	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779526	0.83[JPT][hapmap]
rs3779527	0.91[AMR][1000 genomes]
rs3808055	0.99[ASN][1000 genomes]
rs3808056	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs3808078	0.80[AMR][1000 genomes]
rs3808086	0.82[AMR][1000 genomes]
rs3808088	0.81[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes]
rs3823995	0.83[JPT][hapmap]
rs62481450	0.80[AMR][1000 genomes]
rs6467155	0.91[AMR][1000 genomes]
rs6467156	0.91[AMR][1000 genomes]
rs6969233	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6973092	0.83[JPT][hapmap]
rs7789322	0.90[AMR][1000 genomes]
rs9791922	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3779522	CCDC136	cis	parietal	SCAN
rs3779522	TCN2	trans	lymphoblastoid	seeQTL
rs3779522	GCC1	cis	lymphoblastoid	seeQTL
rs3779522	GPR37	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127669400-127726600	Weak transcription	Hela-S3	cervix
2	chr7:127669600-127718200	Weak transcription	A549	lung
3	chr7:127673200-127712000	Weak transcription	Esophagus	oesophagus
4	chr7:127673800-127715400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr7:127681000-127716200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:127681200-127718200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:127681600-127714600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:127683000-127708800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr7:127685000-127710400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:127689400-127717000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr7:127692800-127714400	Weak transcription	Right Ventricle	heart
12	chr7:127692800-127724200	Weak transcription	Right Atrium	heart
13	chr7:127693200-127718400	Weak transcription	HMEC	breast
14	chr7:127693400-127708800	Strong transcription	Fetal Intestine Small	intestine
15	chr7:127693400-127711600	Weak transcription	Adipose Nuclei	Adipose
16	chr7:127693400-127714200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:127693400-127716600	Weak transcription	Colonic Mucosa	Colon
18	chr7:127693400-127717200	Weak transcription	Small Intestine	intestine
19	chr7:127693600-127710200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:127694400-127707400	Weak transcription	Placenta	Placenta
21	chr7:127694400-127713600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:127694400-127716800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr7:127694600-127707200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:127694600-127707400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:127694800-127717200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:127695200-127718000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:127697200-127714800	Weak transcription	HUVEC	blood vessel
28	chr7:127698200-127713600	Weak transcription	Osteobl	bone
29	chr7:127698400-127714600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:127698800-127707600	Weak transcription	HSMMtube	muscle
31	chr7:127699800-127714600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr7:127700000-127712000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:127700400-127711600	Weak transcription	Dnd41	blood
34	chr7:127700400-127714600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:127700400-127714600	Weak transcription	Left Ventricle	heart
36	chr7:127700400-127714800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr7:127700400-127715400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:127700400-127715400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr7:127700800-127711800	Weak transcription	Thymus	Thymus
40	chr7:127701000-127707400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:127701000-127707400	Strong transcription	NHEK	skin
42	chr7:127701000-127712800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr7:127701200-127713000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr7:127701600-127707200	Weak transcription	Fetal Thymus	thymus
45	chr7:127701600-127707600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr7:127701600-127712200	Weak transcription	NHLF	lung
47	chr7:127701600-127724600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:127701800-127714400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr7:127702000-127707200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr7:127702000-127707400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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