Variant report

Variant	rs13008931
Chromosome Location	chr2:189192535-189192536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189155671..189159103-chr2:189189018..189193192,5	K562	blood:

Variant related genes	Relation type
ENSG00000144366	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10174928	0.81[JPT][hapmap]
rs10175259	0.88[ASN][1000 genomes]
rs10180222	0.93[ASN][1000 genomes]
rs10180687	0.81[ASN][1000 genomes]
rs10193506	0.85[CEU][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10197499	0.83[EUR][1000 genomes]
rs10210696	0.81[ASN][1000 genomes]
rs1036649	0.81[ASN][1000 genomes]
rs10804020	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10931343	0.82[ASN][1000 genomes]
rs10931344	0.82[ASN][1000 genomes]
rs10931346	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10931355	0.81[JPT][hapmap]
rs10931356	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10931359	1.00[CEU][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11900558	0.82[ASN][1000 genomes]
rs12329399	0.81[JPT][hapmap]
rs12464904	0.83[ASN][1000 genomes]
rs12465164	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12465625	1.00[CEU][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12469904	0.91[EUR][1000 genomes]
rs12473653	0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12473872	0.82[JPT][hapmap]
rs12474692	1.00[CEU][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12611919	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs12613615	0.93[ASN][1000 genomes]
rs12619361	0.93[ASN][1000 genomes]
rs12624002	0.96[CEU][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12693487	0.82[ASN][1000 genomes]
rs12693489	0.93[ASN][1000 genomes]
rs12987194	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs13014693	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13022513	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13389155	0.81[JPT][hapmap]
rs13424536	0.81[JPT][hapmap]
rs1898986	0.81[ASN][1000 genomes]
rs34189381	0.87[ASN][1000 genomes]
rs34445909	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35180255	0.81[EUR][1000 genomes]
rs35365782	0.86[EUR][1000 genomes]
rs35964306	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4261684	0.81[ASN][1000 genomes]
rs4274570	0.80[JPT][hapmap]
rs4294965	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4361092	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4381753	0.90[EUR][1000 genomes]
rs4396679	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4398237	0.81[JPT][hapmap]
rs4402719	0.95[ASN][1000 genomes]
rs4402720	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4413123	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4426503	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4430902	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4433962	0.81[JPT][hapmap]
rs4500907	0.82[ASN][1000 genomes]
rs4513258	0.81[JPT][hapmap]
rs4516391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4522565	0.81[JPT][hapmap]
rs4564741	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4591312	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4599076	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4610010	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640356	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4641903	0.82[ASN][1000 genomes]
rs4666758	0.81[JPT][hapmap]
rs4666759	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4667215	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667221	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4667222	0.96[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs4992744	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs59106803	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183206	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183212	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62183213	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6434269	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6711822	0.85[ASN][1000 genomes]
rs6712056	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719273	0.82[ASN][1000 genomes]
rs67211370	0.85[ASN][1000 genomes]
rs67240894	0.82[ASN][1000 genomes]
rs6724428	0.81[CEU][hapmap]
rs6724636	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6724867	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6729182	0.81[JPT][hapmap]
rs6739162	0.81[JPT][hapmap]
rs6744150	0.82[ASN][1000 genomes]
rs6744629	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6753371	0.96[CEU][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7420700	0.81[JPT][hapmap]
rs7425596	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564706	0.83[EUR][1000 genomes]
rs7566619	1.00[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7574262	0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs7585703	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs7586390	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7593215	0.81[JPT][hapmap]
rs7593546	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];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598279	0.96[ASN][1000 genomes]
rs7598785	0.82[ASN][1000 genomes]
rs7599516	0.95[ASN][1000 genomes]
rs893745	0.85[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv431890	chr2:189175905-189202876	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1010330	chr2:189182307-189265614	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv584053	chr2:189184422-189245515	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv999135	chr2:189184937-189265614	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv584054	chr2:189185726-189233419	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13008931	TMEM194B	cis	cerebellum	SCAN
rs13008931	GULP1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189183000-189196000	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr2:189183400-189197200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:189183400-189198400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:189183600-189205000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:189183600-189205400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:189183800-189198600	Weak transcription	Ovary	ovary
7	chr2:189187800-189204600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:189188800-189210600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:189189200-189198400	Weak transcription	HUVEC	blood vessel
10	chr2:189189600-189196000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr2:189190000-189192800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:189190400-189193400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:189190400-189194200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr2:189191200-189192600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr2:189191200-189192800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:189191200-189192800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr2:189191200-189192800	Enhancers	A549	lung
18	chr2:189191200-189193000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr2:189191200-189193200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:189191400-189192600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:189191400-189192800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr2:189191400-189192800	Enhancers	Fetal Lung	lung
23	chr2:189191400-189194800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:189191600-189193000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:189191600-189193000	Enhancers	Rectal Smooth Muscle	rectum
26	chr2:189191600-189197200	Weak transcription	Left Ventricle	heart
27	chr2:189191800-189192600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr2:189191800-189192800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:189191800-189195400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:189191800-189197200	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:189191800-189197200	Weak transcription	Psoas Muscle	Psoas
32	chr2:189191800-189197200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:189192000-189192800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:189192000-189192800	Weak transcription	NHDF-Ad	bronchial
35	chr2:189192000-189193600	Enhancers	K562	blood
36	chr2:189192000-189194400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:189192000-189195400	Weak transcription	Fetal Brain Female	brain
38	chr2:189192000-189205000	Weak transcription	Fetal Stomach	stomach
39	chr2:189192200-189193000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr2:189192200-189197200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:189192200-189197200	Weak transcription	Aorta	Aorta
42	chr2:189192200-189197800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:189192200-189198400	Weak transcription	NHLF	lung
44	chr2:189192200-189225200	Weak transcription	Placenta	Placenta
45	chr2:189192400-189192800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:189192400-189193600	Weak transcription	Colon Smooth Muscle	Colon
47	chr2:189192400-189197000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:189192400-189197800	Weak transcription	Brain Anterior Caudate	brain

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