Variant report

Variant	rs8071231
Chromosome Location	chr17:18181794-18181795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18181056..18183487-chr17:18218391..18220269,2	MCF-7	breast:
2	chr17:18178546..18181267-chr17:18181551..18184917,3	MCF-7	breast:
3	chr17:18174943..18176690-chr17:18181695..18183863,2	K562	blood:
4	chr17:18176357..18178339-chr17:18181722..18183407,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177302	Chromatin interaction
ENSG00000176994	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11868259	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870126	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12936652	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12936769	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12937300	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12939259	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939357	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939757	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12945597	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946058	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12949078	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949983	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12952556	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12952667	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563631	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1563633	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979277	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2230154	1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273030	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386456	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2386457	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2386458	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2461837	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs2461838	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs2605142	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746023	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746024	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28419113	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764405	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3783	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794771	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794772	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3829583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4632181	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924750	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924842	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924843	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924847	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924849	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4925160	1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs4925162	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925163	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925167	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925169	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925171	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58215032	0.85[EUR][1000 genomes]
rs643333	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6502643	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502644	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502646	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502649	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66903818	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207306	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7215839	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7222684	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7223122	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068602	0.83[EUR][1000 genomes]
rs8068854	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070633	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8074444	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080966	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921866	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941451	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9898631	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8071231	SHMT1	cis	Muscle Skeletal	GTEx
rs8071231	SHMT1	cis	Nerve Tibial	GTEx
rs8071231	SHMT1	cis	multi-tissue	Pritchard
rs8071231	SHMT1	cis	Artery Tibial	GTEx
rs8071231	SHMT1	cis	Esophagus Muscularis	GTEx
rs8071231	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs8071231	ALKBH5	cis	Esophagus Muscularis	GTEx
rs8071231	LLGL1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18165800-18182800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:18166000-18183800	Weak transcription	Fetal Brain Male	brain
3	chr17:18166200-18183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:18166400-18182600	Strong transcription	Fetal Brain Female	brain
5	chr17:18167000-18188200	Weak transcription	Stomach Mucosa	stomach
6	chr17:18168800-18183200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr17:18171000-18183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr17:18172200-18217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:18172400-18201000	Strong transcription	Fetal Stomach	stomach
10	chr17:18172600-18181800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:18172800-18198400	Strong transcription	Thymus	Thymus
12	chr17:18173000-18198400	Strong transcription	Fetal Thymus	thymus
13	chr17:18173000-18199000	Strong transcription	Primary T cells from cord blood	blood
14	chr17:18173000-18200400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr17:18173000-18213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:18173200-18198400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr17:18173200-18200200	Strong transcription	Placenta	Placenta
18	chr17:18173400-18183600	Weak transcription	Fetal Heart	heart
19	chr17:18173400-18198200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr17:18173400-18198400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr17:18173400-18198800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr17:18173400-18200200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr17:18173400-18200800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:18173400-18201000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr17:18173400-18201000	Strong transcription	Fetal Intestine Small	intestine
26	chr17:18173600-18190800	Strong transcription	A549	lung
27	chr17:18173600-18198200	Strong transcription	Stomach Smooth Muscle	stomach
28	chr17:18173600-18200200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:18173600-18200800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr17:18174000-18200600	Strong transcription	Dnd41	blood
31	chr17:18174200-18200600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr17:18174800-18182400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:18174800-18190600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr17:18174800-18198600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr17:18174800-18200600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr17:18175400-18189400	Strong transcription	NHLF	lung
37	chr17:18175600-18181800	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr17:18175600-18189200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:18175600-18196600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr17:18175600-18200800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr17:18175800-18181800	Strong transcription	GM12878-XiMat	blood
42	chr17:18175800-18184000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:18175800-18190200	Strong transcription	Brain Germinal Matrix	brain
44	chr17:18175800-18198600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr17:18175800-18199000	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr17:18175800-18200800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:18175800-18201000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:18176200-18182000	Strong transcription	Brain Anterior Caudate	brain
49	chr17:18176200-18182000	Strong transcription	NH-A	brain
50	chr17:18176200-18190800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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