Variant report

Variant	rs2102954
Chromosome Location	chr19:44029744-44029745
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44029421..44031405-chr19:44036593..44038198,2	K562	blood:
2	chr19:44028119..44031033-chr19:44098735..44101211,2	MCF-7	breast:
3	chr19:44006689..44009864-chr19:44027261..44031051,4	MCF-7	breast:
4	chr19:44029247..44034379-chr19:44035166..44038879,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226763	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000176531	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000176472	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12460021	0.85[EUR][1000 genomes]
rs12973764	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs12979907	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12980646	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs12981023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs184239	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs1978008	0.82[EUR][1000 genomes]
rs2682585	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2682586	0.89[CEU][hapmap]
rs2854506	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2854507	0.82[EUR][1000 genomes]
rs2854508	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2854509	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs304731	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs3213295	0.82[EUR][1000 genomes]
rs3213391	0.86[EUR][1000 genomes]
rs34977009	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35016410	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35485252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36075334	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3810381	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4507015	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4544340	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802183	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4802185	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59000923	0.87[EUR][1000 genomes]
rs59827264	0.86[EUR][1000 genomes]
rs61607741	0.87[EUR][1000 genomes]
rs6509094	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71362654	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248167	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap]
rs7248927	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252962	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253177	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253856	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs762506	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs8100211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	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
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2102954	BLOC1S3	cis	parietal	SCAN
rs2102954	ETHE1	cis	lymphoblastoid	seeQTL
rs2102954	LOC653583///PHLDB3	Cis_1M	lymphoblastoid	RTeQTL
rs2102954	ETHE1	Cis_1M	lymphoblastoid	RTeQTL
rs2102954	KCNJ14	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44013200-44029800	Weak transcription	Small Intestine	intestine
2	chr19:44015800-44029800	Weak transcription	Aorta	Aorta
3	chr19:44015800-44030000	Weak transcription	Ovary	ovary
4	chr19:44028600-44030600	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr19:44028600-44030800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr19:44028800-44029800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:44028800-44029800	Enhancers	Primary B cells from peripheral blood	blood
8	chr19:44028800-44029800	Enhancers	Gastric	stomach
9	chr19:44028800-44029800	Flanking Active TSS	NHEK	skin
10	chr19:44028800-44030000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr19:44028800-44030200	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr19:44028800-44030200	Enhancers	Spleen	Spleen
13	chr19:44028800-44030600	Flanking Active TSS	Colonic Mucosa	Colon
14	chr19:44028800-44031800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr19:44028800-44031800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:44029000-44029800	Enhancers	Fetal Muscle Trunk	muscle
17	chr19:44029000-44029800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr19:44029000-44029800	Flanking Active TSS	Hela-S3	cervix
19	chr19:44029000-44029800	Flanking Active TSS	HMEC	breast
20	chr19:44029000-44030000	Flanking Active TSS	HSMM	muscle
21	chr19:44029000-44030400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr19:44029000-44030400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr19:44029000-44030400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:44029000-44030400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr19:44029000-44030800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr19:44029000-44031800	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr19:44029000-44032000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr19:44029200-44029800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:44029200-44029800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:44029200-44030000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:44029200-44030000	Flanking Active TSS	NHDF-Ad	bronchial
32	chr19:44029200-44030200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:44029200-44030400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:44029200-44030800	Flanking Active TSS	HUVEC	blood vessel
35	chr19:44029200-44030800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr19:44029200-44031000	Flanking Active TSS	Liver	Liver
37	chr19:44029200-44031800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:44029200-44032000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:44029200-44032000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:44029200-44032000	Active TSS	Fetal Intestine Large	intestine
41	chr19:44029400-44029800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr19:44029400-44029800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
43	chr19:44029400-44029800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr19:44029400-44029800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr19:44029400-44029800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr19:44029400-44029800	Active TSS	Right Atrium	heart
47	chr19:44029400-44029800	Flanking Active TSS	A549	lung
48	chr19:44029400-44030000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr19:44029400-44030000	Flanking Active TSS	Colon Smooth Muscle	Colon
50	chr19:44029400-44030000	Flanking Active TSS	Rectal Smooth Muscle	rectum

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