Variant report

Variant	rs7025938
Chromosome Location	chr9:103088321-103088322
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103087811..103094429-chr9:103096062..103101866,9	K562	blood:
2	chr9:103085724..103088717-chr9:103090423..103093250,3	K562	blood:
3	chr9:103087213..103089016-chr9:103234506..103236469,2	K562	blood:
4	chr9:103087241..103090159-chr9:103090884..103093840,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241697	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10117799	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118398	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10118701	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120244	0.88[ASN][1000 genomes]
rs10123866	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123913	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124133	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10124893	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10125785	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10739796	0.85[JPT][hapmap]
rs10760724	0.95[ASN][1000 genomes]
rs10819751	0.95[ASN][1000 genomes]
rs10819756	0.82[ASN][1000 genomes]
rs10819759	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10819761	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10819762	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10819764	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10819767	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10989049	0.98[ASN][1000 genomes]
rs10989056	0.88[ASN][1000 genomes]
rs10989064	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10989067	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10989070	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11789196	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336751	0.85[JPT][hapmap]
rs12684939	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1338121	0.85[CHD][hapmap];0.82[GIH][hapmap];0.86[ASN][1000 genomes]
rs1338123	0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs1338124	0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs1338125	0.85[CHD][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs1338126	0.86[ASN][1000 genomes]
rs1415926	0.85[JPT][hapmap]
rs1535667	0.85[JPT][hapmap]
rs1930243	0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1961367	0.88[ASN][1000 genomes]
rs2026999	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2065997	0.85[CHD][hapmap];0.82[GIH][hapmap];0.88[ASN][1000 genomes]
rs2151131	0.85[CHD][hapmap]
rs2210498	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2245216	0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs2417084	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2417176	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2476441	0.85[JPT][hapmap]
rs2485745	0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2491098	0.83[ASN][1000 genomes]
rs2761056	0.85[JPT][hapmap]
rs2787363	0.85[JPT][hapmap]
rs2787364	0.85[JPT][hapmap]
rs2787365	0.85[JPT][hapmap]
rs2787368	0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2787369	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2787370	0.88[ASN][1000 genomes]
rs2787371	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2787372	0.85[CHD][hapmap];0.97[ASN][1000 genomes]
rs2787373	0.97[ASN][1000 genomes]
rs2787374	0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[ASN][1000 genomes]
rs2787375	0.85[CHD][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs2787376	0.90[ASN][1000 genomes]
rs2787377	0.98[ASN][1000 genomes]
rs2787379	0.86[ASN][1000 genomes]
rs2787380	0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs2787381	0.93[ASN][1000 genomes]
rs2787382	0.86[ASN][1000 genomes]
rs2787383	0.95[ASN][1000 genomes]
rs2787384	0.86[ASN][1000 genomes]
rs2787385	0.93[ASN][1000 genomes]
rs2787386	0.83[ASN][1000 genomes]
rs2787388	0.95[ASN][1000 genomes]
rs2787390	0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs2787395	0.85[JPT][hapmap]
rs2787396	0.85[JPT][hapmap]
rs2787397	0.85[JPT][hapmap]
rs2806687	0.85[JPT][hapmap]
rs2806689	0.86[ASN][1000 genomes]
rs2806690	0.84[ASN][1000 genomes]
rs2806691	0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs2806692	0.95[ASN][1000 genomes]
rs2806693	0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2806694	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2806695	0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs2806696	0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs2806699	0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[ASN][1000 genomes]
rs2806700	0.86[ASN][1000 genomes]
rs2806701	0.83[ASN][1000 genomes]
rs2806702	0.85[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2806703	0.87[ASW][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28464821	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813712	0.85[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3923501	0.98[ASN][1000 genomes]
rs4128230	0.95[ASN][1000 genomes]
rs4237194	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4237195	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4237196	0.88[ASN][1000 genomes]
rs4446782	0.98[ASN][1000 genomes]
rs4742782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742783	0.92[ASN][1000 genomes]
rs4742784	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743392	0.98[ASN][1000 genomes]
rs4743393	1.00[CEU][hapmap];0.86[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];0.97[ASN][1000 genomes]
rs4743394	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743395	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743396	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5029342	0.86[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5029343	0.98[ASN][1000 genomes]
rs59242794	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6479008	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479009	0.98[ASN][1000 genomes]
rs6479011	0.87[ASN][1000 genomes]
rs6479013	0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs6479014	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7020988	0.98[ASN][1000 genomes]
rs7021310	0.88[ASN][1000 genomes]
rs7025891	0.87[ASN][1000 genomes]
rs7035619	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036570	0.88[ASN][1000 genomes]
rs7047694	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7048601	0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7472	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849966	0.98[ASN][1000 genomes]
rs7852189	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7854693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860513	0.88[ASN][1000 genomes]
rs7864494	0.85[CHD][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs7866850	0.88[ASN][1000 genomes]
rs7869985	0.88[ASN][1000 genomes]
rs7871702	0.88[ASN][1000 genomes]
rs7874710	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7874900	0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7875775	0.88[ASN][1000 genomes]
rs846752	0.85[JPT][hapmap]
rs846766	0.85[JPT][hapmap]
rs846770	0.85[JPT][hapmap]
rs860171	0.85[JPT][hapmap]
rs914711	0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9299338	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9408998	0.84[ASN][1000 genomes]
rs944710	0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs946054	0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs959893	0.92[ASN][1000 genomes]
rs9775014	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9775182	0.98[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	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1835721	chr9:102991314-103096666	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7025938	TEX10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103044600-103102400	Weak transcription	Stomach Mucosa	stomach
2	chr9:103046400-103104000	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:103046600-103092400	Strong transcription	Fetal Thymus	thymus
4	chr9:103051000-103088800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:103057600-103112600	Weak transcription	Fetal Brain Male	brain
6	chr9:103058400-103092200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:103063800-103093400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:103063800-103106000	Weak transcription	Esophagus	oesophagus
9	chr9:103064000-103100000	Weak transcription	Colonic Mucosa	Colon
10	chr9:103064200-103093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:103064800-103104200	Weak transcription	Right Ventricle	heart
12	chr9:103065000-103114200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr9:103066200-103088400	Weak transcription	Lung	lung
14	chr9:103066200-103100400	Weak transcription	Aorta	Aorta
15	chr9:103066200-103112600	Weak transcription	Pancreas	Pancrea
16	chr9:103066200-103113200	Weak transcription	Spleen	Spleen
17	chr9:103066200-103113800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr9:103066800-103091600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:103067600-103112400	Weak transcription	Small Intestine	intestine
20	chr9:103068200-103094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:103069200-103095400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:103069400-103094800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:103069800-103092000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:103070000-103093800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:103072200-103113800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:103072600-103091800	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:103073800-103088400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:103074000-103113200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:103075200-103088600	Weak transcription	Ovary	ovary
30	chr9:103076600-103097000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:103078400-103100200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:103078400-103111200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr9:103078400-103112200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:103078600-103109000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:103079000-103093000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:103079000-103103600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:103079200-103097000	Weak transcription	Thymus	Thymus
38	chr9:103079800-103107600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:103080000-103108400	Weak transcription	HSMMtube	muscle
40	chr9:103080400-103088400	Weak transcription	HUVEC	blood vessel
41	chr9:103080600-103090800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr9:103080800-103088400	Weak transcription	Brain Angular Gyrus	brain
43	chr9:103080800-103088400	Weak transcription	NH-A	brain
44	chr9:103080800-103092400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:103080800-103100400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr9:103081000-103091000	Weak transcription	Colon Smooth Muscle	Colon
47	chr9:103081000-103104200	Weak transcription	Fetal Heart	heart
48	chr9:103081200-103100200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr9:103081200-103104600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr9:103081200-103107600	Weak transcription	Stomach Smooth Muscle	stomach

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