Variant report

Variant	rs10255861
Chromosome Location	chr7:127525358-127525359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr7:127525157-127526783	PBDE	blood:	n/a	chr7:127526317-127526327
2	POLR2A	chr7:127524973-127525373	K562	blood:	n/a	n/a
3	USF2	chr7:127525303-127525383	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:127525174..127527787-chr7:127536931..127538683,2	K562	blood:
2	chr7:127524140..127526463-chr7:127531972..127534271,2	MCF-7	breast:
3	chr7:127519364..127522726-chr7:127524466..127527535,4	K562	blood:

Variant related genes	Relation type
SND1	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10215276	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10251423	0.89[ASN][1000 genomes]
rs10260037	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	0.89[ASN][1000 genomes]
rs1075206	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10954163	0.85[ASN][1000 genomes]
rs11521053	0.85[ASN][1000 genomes]
rs1193334	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1193337	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11971935	0.85[ASN][1000 genomes]
rs11972774	0.85[ASN][1000 genomes]
rs11977012	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11977915	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11980318	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12531440	0.85[ASN][1000 genomes]
rs12533846	0.85[ASN][1000 genomes]
rs12539728	0.85[ASN][1000 genomes]
rs12540865	0.85[ASN][1000 genomes]
rs13236900	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13237048	0.85[ASN][1000 genomes]
rs1362267	0.89[EUR][1000 genomes]
rs1362268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[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];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs141450	0.85[ASN][1000 genomes]
rs1419969	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17151241	0.85[ASN][1000 genomes]
rs17151270	0.85[ASN][1000 genomes]
rs17676908	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17676986	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17716738	0.85[AMR][1000 genomes]
rs17718395	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17733988	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1833147	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1860934	0.89[ASN][1000 genomes]
rs2014583	0.83[ASN][1000 genomes]
rs325440	0.85[ASN][1000 genomes]
rs325442	0.89[ASN][1000 genomes]
rs325444	0.89[ASN][1000 genomes]
rs325445	0.89[ASN][1000 genomes]
rs325446	0.89[ASN][1000 genomes]
rs325447	0.89[ASN][1000 genomes]
rs325451	0.89[ASN][1000 genomes]
rs35121681	0.81[ASN][1000 genomes]
rs35971861	0.85[ASN][1000 genomes]
rs3757757	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3757767	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3779529	0.89[ASN][1000 genomes]
rs3779530	0.89[ASN][1000 genomes]
rs3808057	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3808058	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3808073	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3808084	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3808087	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3808092	0.81[ASN][1000 genomes]
rs3808093	0.85[ASN][1000 genomes]
rs3808095	0.85[ASN][1000 genomes]
rs3808097	0.85[ASN][1000 genomes]
rs3808105	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3824000	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4728077	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58583807	0.85[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];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6961381	0.85[ASN][1000 genomes]
rs6963455	0.85[ASN][1000 genomes]
rs6963614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6968199	0.85[ASN][1000 genomes]
rs712716	0.90[JPT][hapmap]
rs717944	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs720300	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73234861	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73234862	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73234876	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73234897	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73238074	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs741599	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs759056	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7786041	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7797663	0.82[ASN][1000 genomes]
rs887745	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs917831	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs917832	0.89[ASN][1000 genomes]
rs918793	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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
rs10255861	TPI1P2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127485200-127527800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:127491400-127527800	Weak transcription	Liver	Liver
3	chr7:127498800-127525600	Weak transcription	Fetal Stomach	stomach
4	chr7:127500200-127535400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:127500400-127527800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr7:127500400-127527800	Weak transcription	Dnd41	blood
7	chr7:127500400-127528000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr7:127500600-127527400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr7:127501000-127527800	Weak transcription	Fetal Thymus	thymus
10	chr7:127505400-127537800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:127505600-127528400	Weak transcription	Hela-S3	cervix
12	chr7:127505800-127539600	Weak transcription	Small Intestine	intestine
13	chr7:127505800-127542000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:127512600-127528000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr7:127514800-127531000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr7:127515400-127527800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:127515400-127540600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:127516000-127527000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr7:127516000-127527800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr7:127516000-127528000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:127516400-127525400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:127516400-127528600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr7:127516400-127540200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr7:127518400-127525600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:127518400-127527000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:127518400-127528200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:127518600-127528000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:127518800-127527000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr7:127518800-127527800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:127519800-127527800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr7:127519800-127527800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:127521800-127529800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr7:127522000-127526400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:127522200-127525800	Weak transcription	Brain Germinal Matrix	brain
35	chr7:127522200-127526800	Enhancers	Brain Cingulate Gyrus	brain
36	chr7:127522200-127527200	Weak transcription	Thymus	Thymus
37	chr7:127522200-127527600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr7:127522400-127525400	Weak transcription	Spleen	Spleen
39	chr7:127522400-127525600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr7:127522400-127525600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr7:127522400-127525800	Weak transcription	Fetal Brain Female	brain
42	chr7:127522400-127527800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr7:127522400-127530200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr7:127522800-127526000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:127523000-127525400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr7:127523000-127525400	Genic enhancers	HSMM	muscle
47	chr7:127523000-127525600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:127523000-127527200	Enhancers	Brain Hippocampus Middle	brain
49	chr7:127523200-127525600	Genic enhancers	K562	blood
50	chr7:127523200-127531200	Weak transcription	Fetal Kidney	kidney

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