Variant report

Variant	rs10797972
Chromosome Location	chr1:184475163-184475164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184473276..184475558-chr1:184475798..184477583,2	MCF-7	breast:
2	chr1:184470841..184472476-chr1:184474091..184476482,2	MCF-7	breast:
3	chr1:184471150..184473758-chr1:184474593..184476421,2	K562	blood:
4	chr1:184461404..184463395-chr1:184472896..184475254,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1007224	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs10737253	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10797971	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911606	0.81[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs11588922	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12125349	0.91[ASN][1000 genomes]
rs12127674	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1339563	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1339564	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1339565	0.91[ASN][1000 genomes]
rs1339566	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs1416751	0.92[CEU][hapmap]
rs1416752	0.81[CHD][hapmap]
rs1569842	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884200	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2001270	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2038307	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2038308	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap]
rs2180073	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs2180077	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2207528	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2378888	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2890015	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4650667	0.94[ASN][1000 genomes]
rs4651208	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.87[ASN][1000 genomes]
rs4651210	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.86[ASN][1000 genomes]
rs4651211	0.87[ASN][1000 genomes]
rs4651213	0.81[CHD][hapmap]
rs4651216	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651217	0.91[ASN][1000 genomes]
rs55729410	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6661707	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6666704	0.87[ASN][1000 genomes]
rs7517518	0.88[ASN][1000 genomes]
rs7533466	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7544240	0.91[ASN][1000 genomes]
rs9633308	0.92[CEU][hapmap];0.81[CHD][hapmap];0.81[EUR][1000 genomes]
rs9970984	0.94[ASN][1000 genomes]
rs9970990	0.94[ASN][1000 genomes]

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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10797972	TDRD5	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184455200-184482000	Weak transcription	Esophagus	oesophagus
2	chr1:184456400-184502200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:184459600-184483000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:184461000-184482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:184461600-184475400	Weak transcription	NHEK	skin
6	chr1:184461600-184476800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:184461600-184479000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:184461600-184502800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:184463800-184476400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:184464200-184475800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:184464400-184476400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:184464400-184478400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:184467800-184475200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:184468000-184482800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:184469400-184476400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:184469400-184478200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:184473600-184475800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:184473600-184476400	Weak transcription	Brain Anterior Caudate	brain
19	chr1:184473600-184476400	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:184473600-184476400	Weak transcription	Small Intestine	intestine
21	chr1:184473600-184476600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:184473600-184478400	Weak transcription	Lung	lung
23	chr1:184473600-184489400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:184473800-184476400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:184473800-184476400	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:184473800-184476800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:184473800-184476800	Weak transcription	HSMMtube	muscle
28	chr1:184473800-184480200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:184473800-184483000	Weak transcription	Colonic Mucosa	Colon
30	chr1:184474000-184475800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:184474000-184475800	Weak transcription	HSMM	muscle
32	chr1:184474000-184476400	Weak transcription	Stomach Mucosa	stomach
33	chr1:184474000-184477200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:184474200-184476400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:184474200-184476400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:184474200-184476400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:184474200-184476400	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:184474200-184476400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:184474200-184476400	Weak transcription	Fetal Stomach	stomach
40	chr1:184474200-184476600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:184474200-184476800	Weak transcription	Fetal Brain Female	brain
42	chr1:184474200-184476800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:184474200-184477000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:184474200-184478600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:184474200-184482000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:184474200-184488600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:184474400-184475400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:184474400-184475800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:184474400-184475800	Weak transcription	Right Atrium	heart
50	chr1:184474400-184476200	Weak transcription	Fetal Heart	heart

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