Variant report

Variant	rs2817978
Chromosome Location	chr1:213373306-213373307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10127851	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10864034	0.86[AMR][1000 genomes]
rs10864036	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10864038	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120082	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs11120102	0.85[EUR][1000 genomes]
rs1391549	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391550	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1498357	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1566247	0.86[AMR][1000 genomes]
rs17020338	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1995151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173398	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2494767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2647387	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817976	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2817981	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2817984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2841425	0.96[ASN][1000 genomes]
rs2841427	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2841439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002285	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3010787	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs3124668	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs4655386	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951476	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs4951479	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs4951662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs4951677	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6419469	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6419470	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6540778	0.85[AMR][1000 genomes]
rs6540780	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6540781	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6540782	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6657234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6658259	0.84[AMR][1000 genomes]
rs6666814	0.85[AMR][1000 genomes]
rs6671872	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];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6691488	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs6692056	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6692144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6693291	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697921	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs6699158	0.82[AMR][1000 genomes]
rs6700169	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535369	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7547274	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9308430	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9429901	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9429902	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9430118	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9430120	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9430121	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9430122	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9430123	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392967	chr1:213271844-213490132	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv1794228	chr1:213355519-213379480	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1012014	chr1:213371127-213423214	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2817978	KCNH1	cis	cerebellum	SCAN
rs2817978	ANGEL2	cis	cerebellum	SCAN
rs2817978	ANGEL2	cis	parietal	SCAN
rs2817978	RPS6KC1	cis	Artery Tibial	GTEx
rs2817978	SNORA16B	cis	cerebellum	SCAN
rs2817978	ANGEL2	cis	Esophagus Mucosa	GTEx
rs2817978	BATF3	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213301000-213374800	Weak transcription	HSMM	muscle
2	chr1:213326600-213422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:213328200-213387200	Weak transcription	Spleen	Spleen
4	chr1:213337800-213374400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:213340600-213424600	Weak transcription	Pancreas	Pancrea
6	chr1:213345600-213404600	Weak transcription	Osteobl	bone
7	chr1:213346200-213387400	Weak transcription	Gastric	stomach
8	chr1:213350400-213383200	Weak transcription	Placenta	Placenta
9	chr1:213357800-213387200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:213358000-213375000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:213360400-213405200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:213360600-213378000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:213361600-213386600	Weak transcription	Aorta	Aorta
14	chr1:213362200-213415400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:213368200-213378200	Weak transcription	K562	blood
16	chr1:213368200-213386600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:213368200-213387200	Weak transcription	Lung	lung
18	chr1:213369600-213388800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:213369800-213398200	Weak transcription	Fetal Heart	heart
20	chr1:213370000-213374400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:213370600-213380200	Weak transcription	Fetal Stomach	stomach
22	chr1:213370800-213380600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:213370800-213427600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:213371000-213389400	Weak transcription	Right Ventricle	heart
25	chr1:213371400-213374600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:213371600-213373400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:213371600-213374400	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr1:213371600-213385000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:213371600-213385400	Weak transcription	NHDF-Ad	bronchial
30	chr1:213371800-213373400	Strong transcription	Adipose Nuclei	Adipose
31	chr1:213371800-213373400	Strong transcription	Fetal Lung	lung
32	chr1:213371800-213374400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:213371800-213378000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:213371800-213386000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:213371800-213387200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:213371800-213388800	Weak transcription	HepG2	liver
37	chr1:213371800-213390000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:213372000-213389800	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:213372000-213393200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:213372000-213405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:213372600-213377400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:213372600-213390200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:213372600-213413800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:213372800-213374400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:213372800-213377800	Weak transcription	Fetal Kidney	kidney
46	chr1:213372800-213387200	Weak transcription	Liver	Liver
47	chr1:213372800-213414000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:213373000-213373400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:213373000-213373800	Weak transcription	Primary T cells from cord blood	blood
50	chr1:213373000-213374000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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