Variant report

Variant	rs7778955
Chromosome Location	chr7:39740487-39740488
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	chr7:39739429..39741292-chr7:39741440..39743225,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228554	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10253933	1.00[ASN][1000 genomes]
rs10267545	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10486803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10486805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11765970	0.95[ASN][1000 genomes]
rs11773499	1.00[JPT][hapmap]
rs11773617	0.95[ASN][1000 genomes]
rs12668144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12669963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12701755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12701756	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701757	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701759	0.95[ASN][1000 genomes]
rs13247563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17417049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17417084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34063025	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34910913	0.95[ASN][1000 genomes]
rs35314132	0.96[ASN][1000 genomes]
rs35774126	0.83[ASN][1000 genomes]
rs35943406	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3779200	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[ASN][1000 genomes]
rs6462940	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6968684	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6976944	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6977082	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.83[ASN][1000 genomes]
rs7779169	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7797693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9648483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7778955	RALA	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
2	chr7:39723600-39742800	Weak transcription	Brain Angular Gyrus	brain
3	chr7:39723800-39743000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:39724200-39741200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:39726600-39742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:39727400-39741600	Strong transcription	Fetal Muscle Leg	muscle
7	chr7:39727400-39747800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:39727600-39741200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr7:39729000-39742400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:39730000-39741600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr7:39730600-39749200	Weak transcription	Ovary	ovary
12	chr7:39731400-39740800	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr7:39732000-39748000	Strong transcription	HUVEC	blood vessel
14	chr7:39732000-39749200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:39732800-39741000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:39733000-39741600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:39734200-39746200	Weak transcription	Fetal Kidney	kidney
18	chr7:39734600-39743000	Strong transcription	HSMM	muscle
19	chr7:39735200-39741400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr7:39735400-39740600	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr7:39735600-39740800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:39735600-39740800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:39735600-39740800	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr7:39735600-39740800	Strong transcription	NHLF	lung
25	chr7:39735600-39741200	Strong transcription	Fetal Intestine Large	intestine
26	chr7:39735600-39741200	Strong transcription	NH-A	brain
27	chr7:39735600-39741400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:39735600-39741600	Strong transcription	HSMMtube	muscle
29	chr7:39735600-39742000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:39735600-39742600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:39735600-39743200	Strong transcription	Primary B cells from cord blood	blood
32	chr7:39735600-39743400	Strong transcription	Primary T cells from cord blood	blood
33	chr7:39735800-39740600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr7:39735800-39741200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:39735800-39741200	Strong transcription	Dnd41	blood
36	chr7:39735800-39741400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:39735800-39741600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr7:39736000-39741600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:39736000-39743600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr7:39736200-39740800	Strong transcription	Liver	Liver
41	chr7:39736200-39740800	Strong transcription	GM12878-XiMat	blood
42	chr7:39736400-39740800	Strong transcription	Thymus	Thymus
43	chr7:39736400-39741000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:39736400-39741400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr7:39736600-39741200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr7:39736600-39749400	Weak transcription	Fetal Heart	heart
47	chr7:39736800-39740800	Strong transcription	Left Ventricle	heart
48	chr7:39737000-39740800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:39737000-39740800	Strong transcription	Right Ventricle	heart
50	chr7:39737200-39741200	Strong transcription	Osteobl	bone

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