Variant report

Variant	rs7893
Chromosome Location	chr2:211296239-211296240
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	chr2:211293517..211296433-chr2:211339377..211342364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115365	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10182794	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10183539	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1019394	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10200430	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1044708	0.85[LWK][hapmap]
rs1044710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932330	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13003388	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13420747	0.91[CEU][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1350462	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1458278	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1902939	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1902940	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2021215	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2370953	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3911559	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4673522	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4673523	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57910651	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58025921	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6726864	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73069721	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7601667	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1012567	chr2:211087588-211315554	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv875767	chr2:211119233-211334647	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv3147	chr2:211281479-211326844	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7893	CRYGB	cis	cerebellum	SCAN
rs7893	LANCL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211287200-211298200	Weak transcription	HMEC	breast
2	chr2:211287200-211299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:211287200-211299600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:211287400-211297800	Weak transcription	NH-A	brain
5	chr2:211288400-211296600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:211290600-211299000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:211291400-211297200	Weak transcription	Ovary	ovary
8	chr2:211291400-211299400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:211291600-211296400	Weak transcription	Osteobl	bone
10	chr2:211291600-211299000	Weak transcription	Lung	lung
11	chr2:211291600-211300800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:211291800-211299600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:211292200-211297400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:211292200-211297400	Weak transcription	Thymus	Thymus
15	chr2:211292400-211323000	Weak transcription	Fetal Brain Male	brain
16	chr2:211293000-211299400	Weak transcription	Esophagus	oesophagus
17	chr2:211293000-211305800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:211293200-211297000	Weak transcription	Psoas Muscle	Psoas
19	chr2:211293200-211297200	Weak transcription	Aorta	Aorta
20	chr2:211293200-211297200	Weak transcription	Left Ventricle	heart
21	chr2:211293200-211297800	Weak transcription	Fetal Kidney	kidney
22	chr2:211293200-211299000	Weak transcription	Brain Germinal Matrix	brain
23	chr2:211293200-211299000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:211293200-211299200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:211293200-211307400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr2:211293200-211307800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:211293200-211311600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:211293400-211299000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:211293600-211299000	Weak transcription	Pancreas	Pancrea
30	chr2:211293800-211297600	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:211293800-211297800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:211293800-211298400	Weak transcription	Hela-S3	cervix
33	chr2:211293800-211299400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:211293800-211299400	Weak transcription	Spleen	Spleen
35	chr2:211293800-211335400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:211294200-211296800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:211294200-211297200	Weak transcription	Gastric	stomach
38	chr2:211294200-211297200	Weak transcription	HepG2	liver
39	chr2:211294200-211299200	Enhancers	Fetal Heart	heart
40	chr2:211294200-211301400	Strong transcription	Primary T cells from cord blood	blood
41	chr2:211294400-211296400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:211294400-211296800	Weak transcription	Brain Substantia Nigra	brain
43	chr2:211294400-211303400	Weak transcription	NHLF	lung
44	chr2:211294600-211297400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:211294600-211297400	Weak transcription	A549	lung
46	chr2:211294800-211306200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:211294800-211306400	Strong transcription	Dnd41	blood
48	chr2:211294800-211322200	Weak transcription	K562	blood
49	chr2:211294800-211333200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:211295000-211297200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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