Variant report

Variant	rs550564
Chromosome Location	chr8:95911749-95911750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:95910082..95911889-chr8:96150413..96152348,2	K562	blood:
2	chr8:95911691..95914398-chr8:95917763..95919672,2	K562	blood:
3	chr8:95910895..95913798-chr8:95915630..95917632,3	K562	blood:
4	chr8:95895328..95898333-chr8:95910317..95912893,3	MCF-7	breast:
5	chr8:95909200..95911980-chr8:96146121..96148321,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INTS8-3	chr8:95911394-95912011	NONHSAT127805

Variant related genes	Relation type
ENSG00000175895	Chromatin interaction
ENSG00000272509	Chromatin interaction
ENSG00000238791	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10086284	0.92[CHB][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs10091683	0.89[EUR][1000 genomes]
rs10098778	0.92[CHB][hapmap]
rs10099941	0.92[CHB][hapmap]
rs10104909	0.92[CHB][hapmap]
rs1011795	0.82[JPT][hapmap]
rs1011796	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs10441538	0.84[CHB][hapmap]
rs10956928	0.89[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10956929	0.87[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10956930	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10956931	0.91[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10956932	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11784717	0.82[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs12541035	0.95[ASN][1000 genomes]
rs12545596	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12548367	0.99[ASN][1000 genomes]
rs12548999	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs12549003	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs12550765	0.91[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs12677346	0.88[EUR][1000 genomes]
rs12679044	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs13271644	0.85[CHB][hapmap]
rs1453377	0.92[CHB][hapmap]
rs1453379	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs16893776	0.92[CHB][hapmap]
rs2123647	0.88[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2278891	0.87[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2340583	0.85[ASN][1000 genomes]
rs2924477	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2924478	0.82[ASN][1000 genomes]
rs2945554	0.88[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2945563	0.91[ASN][1000 genomes]
rs2956210	0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs2956216	0.91[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3019175	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3019182	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34293080	0.95[ASN][1000 genomes]
rs3802193	0.92[CHB][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs4075835	0.86[CHB][hapmap]
rs4570121	0.97[ASN][1000 genomes]
rs4734291	0.87[JPT][hapmap]
rs4735310	0.90[EUR][1000 genomes]
rs4735312	0.91[EUR][1000 genomes]
rs4735328	0.82[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs4735329	0.96[ASN][1000 genomes]
rs4735330	0.99[ASN][1000 genomes]
rs4735331	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4735332	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4735334	0.82[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap]
rs4735336	0.92[CHB][hapmap]
rs4735337	0.92[CHB][hapmap]
rs4735339	0.92[CHB][hapmap]
rs477653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535322	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550418	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551270	0.87[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61537129	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6471497	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs6471498	0.91[EUR][1000 genomes]
rs6471499	0.87[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs6471500	0.87[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6471501	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6471503	0.92[CHB][hapmap]
rs683832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6982393	0.92[CHB][hapmap]
rs6983000	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6987256	0.92[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6987400	0.99[ASN][1000 genomes]
rs7001535	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7002058	0.83[CHB][hapmap]
rs7005317	0.82[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7013163	0.82[EUR][1000 genomes]
rs7015841	0.88[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7017487	0.88[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs713113	0.86[CHB][hapmap]
rs726816	0.84[CHB][hapmap]
rs7820818	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7827478	0.92[CHB][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs7839728	0.88[EUR][1000 genomes]
rs7845219	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs896851	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9643350	0.94[ASN][1000 genomes]
rs9643351	0.99[ASN][1000 genomes]
rs9643352	0.99[ASN][1000 genomes]
rs9643353	0.82[GIH][hapmap];0.82[JPT][hapmap]

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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv891203	chr8:95883232-95948202	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv891204	chr8:95883232-95965135	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs550564	SLC26A7	cis	parietal	SCAN
rs550564	TP53INP1	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95909400-95912000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:95909400-95916800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr8:95909400-95917200	Weak transcription	Fetal Intestine Small	intestine
4	chr8:95909400-95917600	Weak transcription	Pancreas	Pancrea
5	chr8:95909400-95918000	Weak transcription	Gastric	stomach
6	chr8:95909400-95920800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:95909400-95932600	Weak transcription	Esophagus	oesophagus
8	chr8:95909400-95939000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr8:95909400-95941000	Weak transcription	Ovary	ovary
10	chr8:95909400-95941200	Weak transcription	Fetal Stomach	stomach
11	chr8:95909600-95912000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:95909600-95913200	Weak transcription	Fetal Brain Male	brain
13	chr8:95909600-95917800	Weak transcription	Stomach Mucosa	stomach
14	chr8:95909600-95920600	Weak transcription	Brain Angular Gyrus	brain
15	chr8:95909600-95937000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr8:95909600-95938400	Weak transcription	Primary T cells from cord blood	blood
17	chr8:95909600-95941800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr8:95909800-95930400	Weak transcription	Fetal Brain Female	brain
19	chr8:95909800-95940600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr8:95910000-95913800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr8:95910000-95940200	Weak transcription	Thymus	Thymus
22	chr8:95910400-95917200	Weak transcription	Fetal Thymus	thymus
23	chr8:95910400-95918200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:95910800-95911800	Weak transcription	Brain Germinal Matrix	brain
25	chr8:95910800-95912000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr8:95910800-95916800	Weak transcription	Dnd41	blood
27	chr8:95910800-95931600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr8:95910800-95940200	Weak transcription	Hela-S3	cervix
29	chr8:95911000-95911800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr8:95911000-95913800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr8:95911600-95911800	Enhancers	K562	blood

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