Variant report

Variant	rs193
Chromosome Location	chr7:27943809-27943810
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	chr7:27936636..27940623-chr7:27942043..27944252,3	MCF-7	breast:
2	chr7:27933695..27935903-chr7:27942962..27945210,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1055445	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12535525	0.83[ASN][1000 genomes]
rs12666447	0.81[CHD][hapmap]
rs12669526	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17621310	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17621988	0.86[CHD][hapmap];0.81[MKK][hapmap];0.81[ASN][1000 genomes]
rs188	0.87[AMR][1000 genomes]
rs189	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs190	0.84[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs195	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs202	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs204	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs206	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs209	0.90[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs210	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs216	0.81[AMR][1000 genomes]
rs220	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34634838	0.81[ASN][1000 genomes]
rs4719914	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62451117	0.81[ASN][1000 genomes]
rs916855	0.82[AMR][1000 genomes]
rs916856	0.82[AMR][1000 genomes]
rs916857	0.84[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][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	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	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs193	GHRHR	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27926600-27956000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:27930000-27949800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:27937600-27945600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:27937600-27945600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:27937600-27945600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:27937600-27945600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:27937600-27953800	Weak transcription	Right Ventricle	heart
8	chr7:27937600-27956200	Weak transcription	Gastric	stomach
9	chr7:27937800-27945800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:27939000-27945600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:27939000-27946400	Weak transcription	Brain Anterior Caudate	brain
12	chr7:27939200-27953000	Weak transcription	Left Ventricle	heart
13	chr7:27939800-27950200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:27939800-27950400	Weak transcription	Pancreas	Pancrea
15	chr7:27941200-27954400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:27941200-27956200	Weak transcription	Aorta	Aorta
17	chr7:27941400-27945600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:27941400-27945600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:27941400-27945800	Weak transcription	HSMM	muscle
20	chr7:27941400-27946200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr7:27941400-27949800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:27941400-27957600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:27941400-27990800	Weak transcription	Primary T cells from cord blood	blood
24	chr7:27941600-27944600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:27941600-27945800	Weak transcription	Colon Smooth Muscle	Colon
26	chr7:27941600-27947400	Weak transcription	Fetal Lung	lung
27	chr7:27941600-27956000	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:27941600-27962800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:27942200-27945400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:27942200-27945600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr7:27942200-27945800	Weak transcription	Right Atrium	heart
32	chr7:27942200-27945800	Weak transcription	Spleen	Spleen
33	chr7:27942200-27945800	Weak transcription	NHDF-Ad	bronchial
34	chr7:27942200-27949800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:27942200-27950000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:27942200-27953800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:27942200-27956000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr7:27942400-27952400	Weak transcription	Primary B cells from cord blood	blood
39	chr7:27942400-28005600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr7:27942800-27945800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr7:27943600-27948000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:27943800-27945800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:27943800-27947200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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