Variant report

Variant	rs4924750
Chromosome Location	chr17:18260753-18260754
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18259424..18261001-chr17:18264753..18266869,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176974	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11870126	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12936652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12936769	0.83[AMR][1000 genomes]
rs12937300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12939092	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939259	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12939357	0.83[EUR][1000 genomes]
rs12939757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12945597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12946058	0.83[EUR][1000 genomes]
rs12949078	0.81[EUR][1000 genomes]
rs12949983	0.83[EUR][1000 genomes]
rs12952556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12952667	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1563633	0.83[EUR][1000 genomes]
rs1979276	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1979277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2230154	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2273028	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273030	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2386456	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2386457	0.80[EUR][1000 genomes]
rs2461837	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2461838	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2605137	0.83[YRI][hapmap]
rs2605142	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2746023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2746025	0.88[YRI][hapmap]
rs2746027	0.83[YRI][hapmap]
rs3764405	0.83[EUR][1000 genomes]
rs3783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3794771	0.81[EUR][1000 genomes]
rs3794772	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3829583	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4632181	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4924845	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925160	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4925167	0.81[EUR][1000 genomes]
rs4925169	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4925171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4925172	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs643333	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502643	0.80[EUR][1000 genomes]
rs6502644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6502646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6502649	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66903818	0.81[EUR][1000 genomes]
rs672356	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7207123	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7207306	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7215839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7222684	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8070633	0.83[EUR][1000 genomes]
rs8071231	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8073464	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8074444	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8080966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs921865	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs921866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs921986	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs941451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS 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	34 gene(s)	inside rSNPs	diseases
5	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' 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	39 gene(s)	inside rSNPs	diseases
8	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
9	esv2758443	chr17:18234525-18446384	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
10	esv2758677	chr17:18234525-18446384	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	esv1829832	chr17:18235992-18405148	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
12	nsv978377	chr17:18251618-18265255	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv827913	chr17:18253785-18572122	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv1065708	chr17:18259174-18913343	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4924750	SHMT1	cis	Nerve Tibial	GTEx
rs4924750	SHMT1	cis	Esophagus Muscularis	GTEx
rs4924750	SHMT1	cis	Artery Aorta	GTEx
rs4924750	LLGL1	cis	Esophagus Mucosa	GTEx
rs4924750	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs4924750	SHMT1	cis	Whole Blood	GTEx
rs4924750	SHMT1	cis	Artery Tibial	GTEx
rs4924750	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs4924750	ALKBH5	cis	Esophagus Muscularis	GTEx
rs4924750	SHMT1	cis	multi-tissue	Pritchard
rs4924750	LGALS9C	cis	Whole Blood	GTEx
rs4924750	SHMT1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18219400-18266000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18222400-18266200	Weak transcription	Small Intestine	intestine
3	chr17:18223600-18265400	Strong transcription	Fetal Stomach	stomach
4	chr17:18228200-18265800	Weak transcription	Fetal Brain Male	brain
5	chr17:18228600-18266000	Weak transcription	HSMM	muscle
6	chr17:18229000-18266000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:18230200-18265600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:18231000-18266000	Weak transcription	Psoas Muscle	Psoas
9	chr17:18235800-18265400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr17:18242400-18264000	Strong transcription	Fetal Thymus	thymus
11	chr17:18243800-18264200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:18244000-18263800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:18244200-18263800	Strong transcription	Fetal Intestine Small	intestine
14	chr17:18244400-18264200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:18244400-18264200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:18244400-18266200	Weak transcription	Stomach Mucosa	stomach
17	chr17:18245400-18266000	Weak transcription	NH-A	brain
18	chr17:18250200-18265200	Weak transcription	Fetal Kidney	kidney
19	chr17:18250200-18265200	Weak transcription	K562	blood
20	chr17:18250200-18265400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:18250200-18265800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr17:18251000-18265200	Weak transcription	Pancreas	Pancrea
23	chr17:18251000-18265200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr17:18251800-18263800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:18251800-18266000	Weak transcription	Right Ventricle	heart
26	chr17:18252000-18265200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr17:18252000-18265800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:18252000-18266000	Weak transcription	NHLF	lung
29	chr17:18252200-18265800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr17:18252200-18266000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:18252200-18266000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr17:18252400-18265800	Weak transcription	HUVEC	blood vessel
33	chr17:18255600-18265200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr17:18256200-18266000	Weak transcription	Aorta	Aorta
35	chr17:18256800-18261800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr17:18256800-18265200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:18256800-18266000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr17:18256800-18266000	Weak transcription	Colonic Mucosa	Colon
39	chr17:18257000-18261800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr17:18257000-18262000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:18257000-18263600	Weak transcription	Fetal Intestine Large	intestine
42	chr17:18257000-18265000	Weak transcription	Brain Angular Gyrus	brain
43	chr17:18257000-18265200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr17:18257000-18265200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr17:18257000-18265200	Weak transcription	Brain Substantia Nigra	brain
46	chr17:18257000-18265200	Weak transcription	Spleen	Spleen
47	chr17:18257000-18265400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr17:18257000-18265400	Weak transcription	Brain Germinal Matrix	brain
49	chr17:18257000-18265400	Weak transcription	Fetal Brain Female	brain
50	chr17:18257000-18265800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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