Variant report

Variant	rs2854508
Chromosome Location	chr19:44076164-44076165
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44074168..44077284-chr19:44077377..44081867,9	K562	blood:
2	chr19:44074412..44076868-chr19:44077789..44081867,6	K562	blood:

Variant related genes	Relation type
ENSG00000234465	Chromatin interaction
ENSG00000269583	Chromatin interaction
ENSG00000073050	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10402946	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs12973764	0.84[CEU][hapmap]
rs12979907	0.81[EUR][1000 genomes]
rs12980646	0.89[CEU][hapmap]
rs12981023	0.83[CEU][hapmap]
rs12981701	0.81[ASN][1000 genomes]
rs12983281	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1475933	0.84[ASN][1000 genomes]
rs17655646	0.90[CHB][hapmap]
rs184239	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978008	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030404	0.94[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2102954	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2139720	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs25479	0.84[ASN][1000 genomes]
rs25485	0.83[ASN][1000 genomes]
rs2599461	0.80[ASN][1000 genomes]
rs2599462	0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2682563	0.94[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2682585	0.85[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682586	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2854500	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2854501	0.91[ASW][hapmap];0.85[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2854506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2854507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2854509	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304731	0.94[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3213255	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3213263	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3213276	1.00[ASN][1000 genomes]
rs3213295	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3213329	0.85[ASN][1000 genomes]
rs3213333	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3213334	0.92[ASW][hapmap];0.85[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3213356	0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3213387	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34704825	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34977009	0.81[EUR][1000 genomes]
rs35016410	0.82[EUR][1000 genomes]
rs3547	0.84[ASN][1000 genomes]
rs35485252	0.82[EUR][1000 genomes]
rs36075334	0.82[EUR][1000 genomes]
rs3810381	0.82[EUR][1000 genomes]
rs4507015	0.82[EUR][1000 genomes]
rs4544340	0.82[EUR][1000 genomes]
rs4802183	0.84[CEU][hapmap]
rs4802185	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs4803646	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs56012842	0.80[EUR][1000 genomes]
rs6509094	0.82[EUR][1000 genomes]
rs71362654	0.82[EUR][1000 genomes]
rs7248927	0.82[EUR][1000 genomes]
rs7251275	1.00[CHB][hapmap]
rs7252962	0.82[EUR][1000 genomes]
rs7253177	0.81[EUR][1000 genomes]
rs73043690	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs762506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs762507	0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8100211	0.82[EUR][1000 genomes]
rs915927	0.83[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	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1063149	chr19:44059081-44087583	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2854508	GPR4	cis	parietal	SCAN
rs2854508	BLOC1S3	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44039200-44078600	Weak transcription	Hela-S3	cervix
2	chr19:44048400-44078800	Weak transcription	Small Intestine	intestine
3	chr19:44057800-44078800	Weak transcription	HSMMtube	muscle
4	chr19:44058600-44078800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:44059200-44078800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:44059800-44078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:44063400-44076200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:44065200-44078600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:44065400-44078600	Weak transcription	Ovary	ovary
10	chr19:44065400-44078800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:44065400-44078800	Weak transcription	Aorta	Aorta
12	chr19:44065800-44078600	Weak transcription	HSMM	muscle
13	chr19:44066000-44078600	Weak transcription	K562	blood
14	chr19:44066200-44078800	Weak transcription	Pancreas	Pancrea
15	chr19:44066600-44076200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:44066600-44078800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr19:44067000-44078600	Weak transcription	Gastric	stomach
18	chr19:44067200-44076200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:44067200-44078600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr19:44067200-44078600	Weak transcription	Fetal Kidney	kidney
21	chr19:44067400-44076200	Weak transcription	Brain Anterior Caudate	brain
22	chr19:44067400-44078600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:44067400-44078600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:44067400-44078600	Weak transcription	Liver	Liver
25	chr19:44067400-44078600	Weak transcription	Brain Substantia Nigra	brain
26	chr19:44067400-44078600	Weak transcription	Left Ventricle	heart
27	chr19:44067400-44078600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr19:44067400-44078600	Weak transcription	HUVEC	blood vessel
29	chr19:44067400-44078800	Weak transcription	Fetal Heart	heart
30	chr19:44067400-44078800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr19:44067400-44078800	Weak transcription	Right Ventricle	heart
32	chr19:44067600-44078800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:44067800-44077600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:44067800-44078600	Weak transcription	Esophagus	oesophagus
35	chr19:44068000-44077400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr19:44068000-44078600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:44068000-44078600	Weak transcription	Brain Angular Gyrus	brain
38	chr19:44068000-44078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:44068000-44078600	Weak transcription	Spleen	Spleen
40	chr19:44068000-44078600	Weak transcription	NH-A	brain
41	chr19:44068000-44078800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:44068000-44078800	Weak transcription	Lung	lung
43	chr19:44068200-44077400	Weak transcription	GM12878-XiMat	blood
44	chr19:44068200-44077800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:44068200-44078600	Weak transcription	Brain Hippocampus Middle	brain
46	chr19:44068200-44078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:44068200-44078800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr19:44068200-44078800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr19:44068400-44078600	Weak transcription	Colon Smooth Muscle	Colon
50	chr19:44068600-44076200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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