Variant report

Variant	rs172168
Chromosome Location	chr4:129939775-129939776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10028974	0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11098994	0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.88[ASN][1000 genomes]
rs12503465	0.93[YRI][hapmap]
rs12504200	0.81[YRI][hapmap]
rs12512345	0.81[YRI][hapmap]
rs1376202	0.91[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.81[MKK][hapmap];0.81[YRI][hapmap]
rs17416188	0.81[YRI][hapmap]
rs17416706	1.00[YRI][hapmap]
rs1756011	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1757926	0.91[ASN][1000 genomes]
rs1757929	0.91[ASN][1000 genomes]
rs1757936	0.82[JPT][hapmap]
rs1757937	0.92[ASN][1000 genomes]
rs1757938	1.00[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1757942	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1838911	0.92[ASN][1000 genomes]
rs189236	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1900397	0.81[YRI][hapmap]
rs2044523	1.00[YRI][hapmap]
rs2118045	0.94[ASN][1000 genomes]
rs2592948	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2597837	1.00[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2655311	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2777822	0.91[ASN][1000 genomes]
rs2777823	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs280594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs280596	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs280597	0.95[ASN][1000 genomes]
rs280601	1.00[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3099902	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3099903	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3113487	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3113488	0.99[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3113490	0.80[JPT][hapmap]
rs337276	0.94[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap]
rs337279	0.85[ASN][1000 genomes]
rs4975294	0.81[YRI][hapmap]
rs55865936	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs62316971	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62316978	0.91[ASN][1000 genomes]
rs6847784	1.00[YRI][hapmap]
rs7654405	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7671508	0.82[JPT][hapmap]
rs789982	0.82[JPT][hapmap]
rs796886	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs172168	B2M	trans	cerebellum	SCAN
rs172168	SCLT1	cis	cerebellum	SCAN
rs172168	C4orf33	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129917400-129942400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:129932000-129944000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr4:129932200-129947000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:129933200-129942200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:129933400-129942000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:129933400-129942000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr4:129934000-129942400	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:129934200-129942600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:129934200-129944200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:129934600-129944200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr4:129934600-129944200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:129935000-129942200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:129935600-129943400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:129935800-129943800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:129935800-129944400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:129936000-129943400	Weak transcription	Fetal Heart	heart
17	chr4:129936200-129942000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:129936600-129942200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:129936600-129942200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:129936600-129942600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:129936800-129941600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:129936800-129942200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:129936800-129942200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:129936800-129942200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:129936800-129942200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:129936800-129942200	Weak transcription	Dnd41	blood
27	chr4:129936800-129942800	Weak transcription	Placenta	Placenta
28	chr4:129936800-129943800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:129936800-129944000	Weak transcription	NHLF	lung
30	chr4:129937000-129941400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:129937000-129941400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:129937000-129941400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:129937000-129941400	Weak transcription	Fetal Thymus	thymus
34	chr4:129937000-129941600	Weak transcription	Ovary	ovary
35	chr4:129937000-129942000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:129937000-129942000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:129937000-129942000	Weak transcription	Right Ventricle	heart
38	chr4:129937000-129942200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:129937000-129942200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:129937000-129942200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:129937000-129942200	Weak transcription	Esophagus	oesophagus
42	chr4:129937000-129942200	Weak transcription	Pancreas	Pancrea
43	chr4:129937000-129942200	Weak transcription	Thymus	Thymus
44	chr4:129937000-129942200	Weak transcription	Spleen	Spleen
45	chr4:129937000-129942400	Weak transcription	Liver	Liver
46	chr4:129937000-129942600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr4:129937000-129942600	Weak transcription	Left Ventricle	heart
48	chr4:129937000-129942800	Weak transcription	Colonic Mucosa	Colon
49	chr4:129937000-129943000	Weak transcription	Brain Angular Gyrus	brain
50	chr4:129937200-129942000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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