Variant report

Variant	rs73289931
Chromosome Location	chr17:18175656-18175657
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18170342..18172549-chr17:18173949..18176436,3	MCF-7	breast:
2	chr17:18168768..18172845-chr17:18173287..18176443,4	K562	blood:
3	chr17:18174083..18176777-chr17:18181802..18184397,2	MCF-7	breast:
4	chr17:18171240..18173650-chr17:18173908..18177269,4	MCF-7	breast:
5	chr17:18173874..18176766-chr17:18191983..18193813,2	K562	blood:
6	chr17:18174943..18176690-chr17:18181695..18183863,2	K562	blood:
7	chr17:18173960..18176627-chr17:18178120..18180882,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177302	Chromatin interaction
ENSG00000260647	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11555081	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601400	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12601687	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12602780	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12603682	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12603700	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17732686	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17805907	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17806489	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2273026	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2294914	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088175	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794773	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3889402	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925157	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55793748	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55844190	0.83[EUR][1000 genomes]
rs55912774	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55940735	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56018054	0.83[EUR][1000 genomes]
rs56074845	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56159325	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56230317	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56355515	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56360702	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57476545	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58042962	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60435159	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67826234	0.97[ASN][1000 genomes]
rs68165736	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7216214	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7217566	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72831943	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73289935	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73289939	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73289960	0.88[AFR][1000 genomes];0.95[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	nsv1066718	chr17:18125122-18180807	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs73289931	SHMT1	cis	Whole Blood	GTEx
rs73289931	SMCR7	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18165000-18176600	Weak transcription	HUVEC	blood vessel
2	chr17:18165200-18176400	Weak transcription	K562	blood
3	chr17:18165400-18177600	Weak transcription	Small Intestine	intestine
4	chr17:18165600-18181400	Weak transcription	Psoas Muscle	Psoas
5	chr17:18165800-18175800	Weak transcription	GM12878-XiMat	blood
6	chr17:18165800-18182800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:18166000-18179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:18166000-18183800	Weak transcription	Fetal Brain Male	brain
9	chr17:18166200-18183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:18166400-18182600	Strong transcription	Fetal Brain Female	brain
11	chr17:18167000-18188200	Weak transcription	Stomach Mucosa	stomach
12	chr17:18168800-18176400	Weak transcription	Primary B cells from cord blood	blood
13	chr17:18168800-18177600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr17:18168800-18179200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr17:18168800-18179400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:18168800-18183200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr17:18169000-18175800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr17:18169000-18176200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:18169000-18176200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr17:18169000-18176200	Weak transcription	Brain Substantia Nigra	brain
21	chr17:18169000-18176400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr17:18169000-18176400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr17:18169000-18176400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr17:18169000-18176600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr17:18169000-18176600	Weak transcription	HepG2	liver
26	chr17:18169000-18176600	Weak transcription	HSMMtube	muscle
27	chr17:18169000-18177600	Weak transcription	Aorta	Aorta
28	chr17:18169000-18177600	Weak transcription	Esophagus	oesophagus
29	chr17:18169000-18177600	Weak transcription	Gastric	stomach
30	chr17:18169000-18177600	Weak transcription	Ovary	ovary
31	chr17:18169000-18177600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr17:18169000-18177600	Weak transcription	Right Ventricle	heart
33	chr17:18169000-18181200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr17:18169200-18175800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr17:18169200-18176200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:18169200-18176200	Weak transcription	Colonic Mucosa	Colon
37	chr17:18169200-18176400	Weak transcription	Adipose Nuclei	Adipose
38	chr17:18169200-18176400	Weak transcription	Liver	Liver
39	chr17:18169200-18176400	Weak transcription	Brain Angular Gyrus	brain
40	chr17:18169200-18176400	Weak transcription	Fetal Intestine Large	intestine
41	chr17:18169200-18176400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr17:18169200-18176600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr17:18169200-18177400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr17:18169200-18177400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr17:18169200-18177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr17:18169200-18177600	Weak transcription	Left Ventricle	heart
47	chr17:18169200-18177600	Weak transcription	Pancreas	Pancrea
48	chr17:18169200-18179400	Weak transcription	NHDF-Ad	bronchial
49	chr17:18169400-18177600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:18169600-18177400	Weak transcription	Colon Smooth Muscle	Colon

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