Variant report

Variant	rs17676986
Chromosome Location	chr7:127636958-127636959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127635606..127639258-chr7:127641258..127643536,3	K562	blood:
2	chr7:127627591..127629980-chr7:127636383..127638800,3	K562	blood:
3	chr7:127632086..127635094-chr7:127636787..127638892,4	K562	blood:
4	chr7:127622847..127627413-chr7:127635236..127639415,6	K562	blood:
5	chr7:127622847..127631238-chr7:127633836..127639415,10	K562	blood:

Variant related genes	Relation type
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10215276	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10255861	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]
rs10260037	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]
rs1075206	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1193334	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1193337	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1362267	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1362268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1362897	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1419969	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17676908	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17733988	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1833147	0.90[EUR][1000 genomes]
rs3757757	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757767	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3808057	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3808058	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3808073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3808084	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3808087	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3824000	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6948493	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];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6963614	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs720300	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73238074	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs759056	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7786041	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs887745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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	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	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
rs17676986	TPI1P2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127617600-127640600	Weak transcription	Brain Germinal Matrix	brain
2	chr7:127618800-127637800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:127621000-127643600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:127627200-127644800	Weak transcription	Fetal Brain Female	brain
5	chr7:127627600-127637600	Weak transcription	Stomach Mucosa	stomach
6	chr7:127628400-127639400	Strong transcription	GM12878-XiMat	blood
7	chr7:127628400-127648400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:127630200-127638000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr7:127630400-127638800	Strong transcription	Primary B cells from cord blood	blood
10	chr7:127630400-127644000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:127630600-127638600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr7:127630600-127641400	Strong transcription	Primary T cells from cord blood	blood
13	chr7:127631200-127655600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:127631800-127660800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:127632000-127640600	Weak transcription	Gastric	stomach
16	chr7:127632400-127641000	Weak transcription	Colonic Mucosa	Colon
17	chr7:127632400-127643400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr7:127632400-127643600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr7:127632400-127643800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr7:127632600-127657600	Weak transcription	HUVEC	blood vessel
21	chr7:127632800-127639200	Enhancers	Fetal Heart	heart
22	chr7:127633200-127637600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:127633600-127643600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr7:127633800-127638000	Enhancers	Fetal Muscle Leg	muscle
25	chr7:127634000-127641000	Weak transcription	Hela-S3	cervix
26	chr7:127634200-127643400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:127634200-127643600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr7:127634200-127657800	Weak transcription	NH-A	brain
29	chr7:127634400-127637000	Weak transcription	Dnd41	blood
30	chr7:127634400-127637200	Weak transcription	Liver	Liver
31	chr7:127634400-127637800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:127634400-127639400	Weak transcription	Fetal Intestine Large	intestine
33	chr7:127634400-127640600	Weak transcription	Esophagus	oesophagus
34	chr7:127634400-127641400	Weak transcription	NHEK	skin
35	chr7:127634600-127637000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:127634600-127639600	Weak transcription	Fetal Intestine Small	intestine
37	chr7:127634600-127642600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr7:127634600-127646000	Weak transcription	Thymus	Thymus
39	chr7:127635000-127637000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:127635000-127637000	Enhancers	Brain Cingulate Gyrus	brain
41	chr7:127635000-127637200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:127635000-127637200	Enhancers	Right Atrium	heart
43	chr7:127635000-127637400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:127635000-127637600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr7:127635000-127637800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr7:127635000-127638200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:127635000-127638600	Enhancers	HSMMtube	muscle
48	chr7:127635000-127639000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr7:127635200-127637000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:127635200-127637000	Enhancers	Brain Anterior Caudate	brain

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