Variant report

Variant	rs10260037
Chromosome Location	chr7:127507991-127507992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127489642..127491214-chr7:127507516..127510491,2	K562	blood:
2	chr7:127505544..127508080-chr7:127509583..127511619,2	K562	blood:
3	chr7:127498109..127501021-chr7:127504531..127508086,4	K562	blood:
4	chr7:127506647..127509422-chr7:127514082..127515835,2	K562	blood:
5	chr7:127502110..127504704-chr7:127507082..127510314,3	K562	blood:

Variant related genes	Relation type
ENSG00000240579	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10215276	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10251423	0.92[ASN][1000 genomes]
rs10255861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1029927	0.92[ASN][1000 genomes]
rs1075206	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10954163	0.89[ASN][1000 genomes]
rs11521053	0.89[ASN][1000 genomes]
rs1193334	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1193337	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11971935	0.89[ASN][1000 genomes]
rs11972774	0.89[ASN][1000 genomes]
rs11976946	1.00[JPT][hapmap]
rs11977012	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11977915	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11980318	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12531440	0.89[ASN][1000 genomes]
rs12533846	0.89[ASN][1000 genomes]
rs12539728	0.89[ASN][1000 genomes]
rs12540865	0.89[ASN][1000 genomes]
rs13236900	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13237048	0.89[ASN][1000 genomes]
rs1362267	0.84[EUR][1000 genomes]
rs1362268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1362897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs141450	0.89[ASN][1000 genomes]
rs1419969	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17151241	0.89[ASN][1000 genomes]
rs17151270	0.89[ASN][1000 genomes]
rs17676908	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17676986	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17716738	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17718395	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17733988	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1833147	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1860934	0.92[ASN][1000 genomes]
rs1881084	0.83[ASN][1000 genomes]
rs2014583	0.83[ASN][1000 genomes]
rs325440	0.89[ASN][1000 genomes]
rs325442	0.92[ASN][1000 genomes]
rs325444	0.92[ASN][1000 genomes]
rs325445	0.92[ASN][1000 genomes]
rs325446	0.92[ASN][1000 genomes]
rs325447	0.92[ASN][1000 genomes]
rs325451	0.92[ASN][1000 genomes]
rs35121681	0.85[ASN][1000 genomes]
rs35971861	0.89[ASN][1000 genomes]
rs3757757	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3757767	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3779529	0.92[ASN][1000 genomes]
rs3779530	0.92[ASN][1000 genomes]
rs3808057	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3808058	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3808073	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3808084	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3808087	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3808092	0.85[ASN][1000 genomes]
rs3808093	0.89[ASN][1000 genomes]
rs3808095	0.89[ASN][1000 genomes]
rs3808097	0.89[ASN][1000 genomes]
rs3808105	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3824000	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4728077	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55694225	0.83[ASN][1000 genomes]
rs58583807	0.89[ASN][1000 genomes]
rs6948493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6961381	0.89[ASN][1000 genomes]
rs6963455	0.89[ASN][1000 genomes]
rs6963614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6968199	0.89[ASN][1000 genomes]
rs712716	0.90[JPT][hapmap]
rs717944	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs720300	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73234861	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73234862	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73234876	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73234880	0.83[ASN][1000 genomes]
rs73234882	0.83[ASN][1000 genomes]
rs73234897	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73238074	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs741599	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs759056	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs759843	0.83[ASN][1000 genomes]
rs7786041	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797663	0.85[ASN][1000 genomes]
rs887745	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs917831	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs917832	0.92[ASN][1000 genomes]
rs918793	0.89[ASN][1000 genomes]
rs972088	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs972090	0.81[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	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
rs10260037	TPI1P2	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127485000-127512000	Weak transcription	Aorta	Aorta
2	chr7:127485200-127527800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:127485600-127522000	Weak transcription	Placenta	Placenta
4	chr7:127485800-127515200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:127488200-127516400	Weak transcription	HMEC	breast
6	chr7:127488600-127510000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr7:127488600-127515400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:127489600-127508000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:127490200-127512200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr7:127491200-127512200	Weak transcription	A549	lung
11	chr7:127491400-127515400	Weak transcription	NH-A	brain
12	chr7:127491400-127527800	Weak transcription	Liver	Liver
13	chr7:127494000-127515400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:127496600-127519400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:127498400-127509000	Weak transcription	Left Ventricle	heart
16	chr7:127498600-127525000	Weak transcription	Fetal Intestine Small	intestine
17	chr7:127498800-127509200	Weak transcription	Right Ventricle	heart
18	chr7:127498800-127513400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:127498800-127519400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:127498800-127521800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:127498800-127524600	Weak transcription	Gastric	stomach
22	chr7:127498800-127525600	Weak transcription	Fetal Stomach	stomach
23	chr7:127499000-127512400	Weak transcription	Fetal Intestine Large	intestine
24	chr7:127499600-127511600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:127500200-127521800	Weak transcription	Pancreas	Pancrea
26	chr7:127500200-127535400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr7:127500400-127515000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:127500400-127527800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr7:127500400-127527800	Weak transcription	Dnd41	blood
30	chr7:127500400-127528000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:127500600-127508000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:127500600-127515000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:127500600-127517400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:127500600-127527400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:127501000-127527800	Weak transcription	Fetal Thymus	thymus
36	chr7:127503000-127513800	Weak transcription	Fetal Lung	lung
37	chr7:127503000-127524400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:127503400-127510200	Weak transcription	Psoas Muscle	Psoas
39	chr7:127503400-127517600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr7:127503800-127508200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr7:127504600-127522000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr7:127505000-127510000	Weak transcription	GM12878-XiMat	blood
43	chr7:127505200-127515200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:127505200-127515800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr7:127505400-127516000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr7:127505400-127537800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr7:127505600-127509400	Weak transcription	NHEK	skin
48	chr7:127505600-127513200	Weak transcription	HepG2	liver
49	chr7:127505600-127514000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:127505600-127514000	Weak transcription	NHLF	lung

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