Variant report

Variant	rs937290
Chromosome Location	chr1:45961955-45961956
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45804114..45807301-chr1:45961577..45967419,8	K562	blood:
2	chr1:45960198..45962227-chr1:46049813..46051584,2	K562	blood:
3	chr1:45284333..45287601-chr1:45959122..45962141,3	K562	blood:
4	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
5	chr1:45959289..45962571-chr1:45963704..45967328,6	MCF-7	breast:
6	chr1:45961218..45963399-chr1:45963495..45965607,2	K562	blood:

Variant related genes	Relation type
ENSG00000070759	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10157597	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1044717	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10493120	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs10736426	0.96[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10789466	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1088099	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211110	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs11211113	0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11211132	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11211134	0.91[EUR][1000 genomes]
rs12038608	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12042481	0.85[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs12047498	0.85[ASN][1000 genomes]
rs12048936	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12082256	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12145526	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729974	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12749658	0.91[EUR][1000 genomes]
rs1337902	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];0.95[ASN][1000 genomes]
rs1494813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1691217	0.86[GIH][hapmap];0.89[MEX][hapmap]
rs1765711	1.00[JPT][hapmap]
rs1974271	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2065708	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs2077808	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2152077	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2356555	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2356559	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2356560	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2356561	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2991966	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2993257	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2993259	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34315657	0.81[EUR][1000 genomes]
rs3748643	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4233498	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660306	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660309	0.86[EUR][1000 genomes]
rs4660860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4660862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4660864	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660866	0.86[EUR][1000 genomes]
rs4660867	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4660868	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660871	0.82[EUR][1000 genomes]
rs4660872	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6429566	0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs6429567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6429569	0.96[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6667191	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6673477	0.82[EUR][1000 genomes]
rs6688424	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6688516	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7516006	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7522705	0.96[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7534467	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7536557	0.96[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7539253	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7543076	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7546268	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7549093	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs781059	0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs781060	0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs781061	1.00[JPT][hapmap]
rs781066	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs882803	0.96[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs945179	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9725380	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9803979	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs937290	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs937290	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs937290	CCDC163P	cis	Artery Aorta	GTEx
rs937290	CCDC163P	cis	Heart Left Ventricle	GTEx
rs937290	ST3GAL3	cis	parietal	SCAN
rs937290	CCDC163P	cis	lymphoblastoid	seeQTL
rs937290	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs937290	CYP4A11	cis	parietal	SCAN
rs937290	CCDC163P	cis	Esophagus Muscularis	GTEx
rs937290	CYP4Z2P	cis	parietal	SCAN
rs937290	CCDC163P	cis	Thyroid	GTEx
rs937290	CCDC163P	cis	Artery Tibial	GTEx
rs937290	CCDC163P	cis	Muscle Skeletal	GTEx
rs937290	CCDC163P	cis	Whole Blood	GTEx
rs937290	CCDC163P	cis	Esophagus Mucosa	GTEx
rs937290	BEND5	cis	cerebellum	SCAN
rs937290	CCDC163P	cis	Stomach	GTEx
rs937290	CCDC163P	cis	Nerve Tibial	GTEx
rs937290	CCDC163P	cis	lung	GTEx
rs937290	TESK2	cis	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45964600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:45956800-45964800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:45956800-45964800	Weak transcription	Spleen	Spleen
4	chr1:45956800-45965000	Weak transcription	Gastric	stomach
5	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
6	chr1:45957000-45962600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:45957000-45964200	Weak transcription	Pancreas	Pancrea
8	chr1:45957000-45964400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:45957000-45964600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:45957000-45964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:45957200-45964200	Weak transcription	K562	blood
12	chr1:45957400-45964000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:45957400-45964600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:45957400-45965200	Weak transcription	HSMM	muscle
15	chr1:45957600-45962200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:45957600-45964000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:45957600-45964000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:45957600-45964200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:45957600-45964200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:45957600-45964200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:45957600-45964400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:45957600-45964600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:45957600-45964600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:45957600-45964600	Weak transcription	Ovary	ovary
25	chr1:45957600-45964600	Weak transcription	Thymus	Thymus
26	chr1:45957600-45964600	Weak transcription	Osteobl	bone
27	chr1:45957600-45964800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:45957600-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:45957600-45964800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:45957600-45965000	Weak transcription	Psoas Muscle	Psoas
31	chr1:45957800-45962000	Weak transcription	Placenta	Placenta
32	chr1:45957800-45962200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:45957800-45962200	Weak transcription	Fetal Stomach	stomach
34	chr1:45957800-45964000	Weak transcription	Liver	Liver
35	chr1:45957800-45964000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:45957800-45964000	Weak transcription	Brain Substantia Nigra	brain
37	chr1:45957800-45964200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:45957800-45964400	Weak transcription	Brain Angular Gyrus	brain
39	chr1:45957800-45964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:45957800-45964600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:45957800-45964600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:45957800-45964800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:45957800-45964800	Weak transcription	Fetal Muscle Leg	muscle
44	chr1:45957800-45965000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:45957800-45965000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:45958000-45964000	Weak transcription	Dnd41	blood
47	chr1:45958000-45964200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:45958000-45964200	Weak transcription	GM12878-XiMat	blood
49	chr1:45958000-45964400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:45958000-45964400	Weak transcription	Brain Anterior Caudate	brain

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