Variant report

Variant	rs2991975
Chromosome Location	chr1:46024526-46024527
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
2	chr1:46023197..46024863-chr1:46038353..46040089,2	K562	blood:
3	chr1:45985097..45987613-chr1:46022518..46025124,4	MCF-7	breast:
4	chr1:46013953..46018760-chr1:46019151..46024741,9	K562	blood:
5	chr1:45982318..45989250-chr1:46023024..46029715,13	K562	blood:
6	chr1:46015251..46018245-chr1:46018589..46025048,8	MCF-7	breast:
7	chr1:46013953..46019415-chr1:46020167..46024741,10	K562	blood:
8	chr1:45983804..45987826-chr1:46021822..46025099,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction
ENSG00000117448	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10430123	0.83[JPT][hapmap]
rs10430124	0.83[JPT][hapmap]
rs10749856	0.84[JPT][hapmap]
rs10789467	0.84[JPT][hapmap]
rs10789470	0.83[JPT][hapmap]
rs10890333	0.83[JPT][hapmap]
rs10890336	0.87[JPT][hapmap]
rs11211157	0.83[JPT][hapmap]
rs11211163	0.83[JPT][hapmap]
rs11211166	0.88[JPT][hapmap]
rs12043945	0.84[JPT][hapmap]
rs12049027	0.87[JPT][hapmap]
rs12091503	0.84[JPT][hapmap]
rs1250	0.83[JPT][hapmap]
rs12727696	0.82[EUR][1000 genomes]
rs1547924	0.83[JPT][hapmap]
rs2050376	0.83[JPT][hapmap]
rs2088102	0.91[CEU][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2230657	0.88[CEU][hapmap]
rs2230658	0.83[JPT][hapmap]
rs2230659	0.84[JPT][hapmap]
rs2275085	0.83[JPT][hapmap]
rs2356551	0.81[ASN][1000 genomes]
rs2453404	0.96[ASN][1000 genomes]
rs28647556	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs2934856	0.95[ASN][1000 genomes]
rs2934857	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2934858	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2934859	0.81[CHB][hapmap];0.83[JPT][hapmap];0.98[ASN][1000 genomes]
rs2991970	0.90[ASN][1000 genomes]
rs2991971	0.94[ASN][1000 genomes]
rs2991972	0.81[CHB][hapmap];0.83[JPT][hapmap];0.98[ASN][1000 genomes]
rs2991973	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2991974	0.98[ASN][1000 genomes]
rs2991985	0.82[AMR][1000 genomes]
rs2991986	0.83[JPT][hapmap]
rs2991987	0.89[JPT][hapmap]
rs2993262	0.98[ASN][1000 genomes]
rs2993263	0.81[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3013595	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs3013597	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs3014216	0.92[CEU][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3014218	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3014219	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3014220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014238	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs3014239	0.83[JPT][hapmap]
rs4274104	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs4391704	0.88[CEU][hapmap]
rs4431884	0.83[JPT][hapmap]
rs4468203	0.86[CEU][hapmap];0.94[JPT][hapmap]
rs4559551	0.83[JPT][hapmap]
rs4564187	0.84[JPT][hapmap]
rs4609469	0.84[JPT][hapmap]
rs4660876	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4660882	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs5021934	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs512026	0.81[ASN][1000 genomes]
rs512083	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs518365	0.85[ASN][1000 genomes]
rs523526	0.98[ASN][1000 genomes]
rs592214	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60608374	0.81[ASN][1000 genomes]
rs606542	0.98[ASN][1000 genomes]
rs622798	0.81[CHB][hapmap];0.83[JPT][hapmap];0.98[ASN][1000 genomes]
rs6429576	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs644915	0.84[ASN][1000 genomes]
rs6656279	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs666720	0.82[ASN][1000 genomes]
rs667626	0.98[ASN][1000 genomes]
rs6697821	0.83[JPT][hapmap]
rs7525459	0.82[EUR][1000 genomes]
rs7526665	0.83[ASN][1000 genomes]
rs9147	0.96[ASN][1000 genomes]
rs9429079	0.80[ASN][1000 genomes]
rs9429085	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2991975	CCDC163P	cis	Muscle Skeletal	GTEx
rs2991975	CCDC163P	cis	Heart Left Ventricle	GTEx
rs2991975	CCDC163P	cis	Nerve Tibial	GTEx
rs2991975	CCDC163P	cis	Stomach	GTEx
rs2991975	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs2991975	Hs.396207	cis	multi-tissue	Pritchard
rs2991975	CCDC163P	cis	Esophagus Mucosa	GTEx
rs2991975	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs2991975	CCDC163P	cis	Esophagus Muscularis	GTEx
rs2991975	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs2991975	MAST2	cis	Artery Tibial	GTEx
rs2991975	CCDC163P	cis	lung	GTEx
rs2991975	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs2991975	CCDC163P	cis	Whole Blood	GTEx
rs2991975	CCDC163P	cis	Artery Tibial	GTEx
rs2991975	MAST2	cis	Artery Aorta	GTEx
rs2991975	CCDC163P	cis	Thyroid	GTEx
rs2991975	GPBP1L1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46017000-46025800	Weak transcription	Spleen	Spleen
2	chr1:46017400-46027000	Weak transcription	Aorta	Aorta
3	chr1:46017400-46027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:46017800-46026800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:46017800-46026800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:46017800-46026800	Weak transcription	HSMMtube	muscle
7	chr1:46017800-46027200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:46017800-46027400	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:46017800-46027400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:46017800-46027400	Weak transcription	Gastric	stomach
11	chr1:46017800-46032200	Weak transcription	Brain Anterior Caudate	brain
12	chr1:46017800-46038800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:46018000-46027400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:46018000-46032200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:46018000-46038600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:46018200-46037400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:46018400-46024800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:46018400-46025600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:46018400-46025800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:46018400-46026600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:46018400-46026600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:46018400-46026800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:46018400-46026800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:46018400-46027200	Weak transcription	Fetal Lung	lung
25	chr1:46018400-46027400	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:46018400-46027400	Weak transcription	HUVEC	blood vessel
27	chr1:46018400-46029600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:46018400-46029800	Weak transcription	NHDF-Ad	bronchial
29	chr1:46018400-46032000	Weak transcription	Fetal Kidney	kidney
30	chr1:46018400-46032600	Weak transcription	Fetal Brain Male	brain
31	chr1:46018400-46036400	Strong transcription	Fetal Stomach	stomach
32	chr1:46018400-46036800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:46018400-46036800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:46018400-46036800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:46018400-46037000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:46018600-46026800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:46018600-46026800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:46018600-46027000	Weak transcription	Esophagus	oesophagus
39	chr1:46018600-46032000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:46018600-46034200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:46018600-46036800	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:46018600-46037600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:46018600-46038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:46019200-46032000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:46020200-46026000	Weak transcription	Lung	lung
46	chr1:46020600-46025400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:46020600-46032200	Weak transcription	Brain Angular Gyrus	brain
48	chr1:46020800-46024600	Strong transcription	Fetal Intestine Small	intestine
49	chr1:46021400-46026800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:46021600-46027400	Weak transcription	Primary hematopoietic stem cells	blood

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