Variant report

Variant	rs2472179
Chromosome Location	chr10:38384848-38384849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:38299349..38301423-chr10:38382665..38385531,5	K562	blood:
2	chr10:38298279..38301657-chr10:38381478..38384966,6	MCF-7	breast:
3	chr10:38298494..38301362-chr10:38382665..38385531,3	K562	blood:

Variant related genes	Relation type
ENSG00000189180	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1138252	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1329786	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs176876	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176879	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs176882	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs176885	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs176889	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2008449	0.84[ASN][1000 genomes]
rs2021650	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2023299	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2144859	0.82[ASN][1000 genomes]
rs2178962	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2263162	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2263164	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2384731	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2472177	0.87[ASN][1000 genomes]
rs2472178	0.87[ASN][1000 genomes]
rs2474554	0.81[ASN][1000 genomes]
rs2474564	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2474570	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2474572	0.87[ASN][1000 genomes]
rs2474573	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2474581	0.86[ASN][1000 genomes]
rs2474591	0.84[ASN][1000 genomes]
rs2474596	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2474597	0.84[ASN][1000 genomes]
rs2474610	0.82[ASN][1000 genomes]
rs2504120	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2504121	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2504127	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2504139	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2504141	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505179	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2505185	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2505190	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2505198	0.85[ASN][1000 genomes]
rs2505235	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2505236	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2505244	0.82[ASN][1000 genomes]
rs2505249	0.82[ASN][1000 genomes]
rs2505251	0.82[ASN][1000 genomes]
rs2505252	0.82[ASN][1000 genomes]
rs2505258	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2505259	0.84[ASN][1000 genomes]
rs6482060	0.82[ASN][1000 genomes]
rs7915062	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs932538	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv540566	chr10:38301001-38680127	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv550419	chr10:38311777-38501654	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv6465	chr10:38377662-38422125	Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2472179	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2472179	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38383600-38385600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr10:38383800-38386200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
3	chr10:38384000-38388400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:38384200-38385200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr10:38384200-38385400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr10:38384200-38389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr10:38384200-38389200	Weak transcription	Aorta	Aorta
8	chr10:38384400-38385000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr10:38384400-38385000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr10:38384400-38385000	Weak transcription	Liver	Liver
11	chr10:38384400-38385000	Enhancers	Pancreas	Pancrea
12	chr10:38384400-38385200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr10:38384400-38385400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr10:38384400-38385400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr10:38384400-38385400	Weak transcription	Fetal Kidney	kidney
16	chr10:38384400-38385600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr10:38384400-38385800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr10:38384400-38386000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr10:38384400-38386800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr10:38384400-38388200	Weak transcription	Psoas Muscle	Psoas
21	chr10:38384400-38388800	Weak transcription	Fetal Intestine Small	intestine
22	chr10:38384400-38389200	Weak transcription	Small Intestine	intestine
23	chr10:38384400-38389400	Weak transcription	Thymus	Thymus
24	chr10:38384400-38396400	Weak transcription	HUVEC	blood vessel
25	chr10:38384600-38385000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr10:38384600-38385000	Weak transcription	Brain Anterior Caudate	brain
27	chr10:38384600-38385000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:38384600-38385000	Genic enhancers	Right Ventricle	heart
29	chr10:38384600-38385200	Weak transcription	Primary B cells from cord blood	blood
30	chr10:38384600-38385200	Weak transcription	Primary T cells from cord blood	blood
31	chr10:38384600-38385200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr10:38384600-38385200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr10:38384600-38385200	Weak transcription	Fetal Brain Male	brain
34	chr10:38384600-38385200	Weak transcription	Lung	lung
35	chr10:38384600-38385200	Weak transcription	HSMM	muscle
36	chr10:38384600-38385200	Weak transcription	NHEK	skin
37	chr10:38384600-38385400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:38384600-38385400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:38384600-38385400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr10:38384600-38385400	Weak transcription	Colon Smooth Muscle	Colon
41	chr10:38384600-38385400	Weak transcription	Fetal Thymus	thymus
42	chr10:38384600-38385400	Weak transcription	Ovary	ovary
43	chr10:38384600-38385400	Weak transcription	Hela-S3	cervix
44	chr10:38384600-38385600	Enhancers	HepG2	liver
45	chr10:38384600-38386200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr10:38384600-38386200	Strong transcription	HSMMtube	muscle
47	chr10:38384600-38386600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr10:38384600-38386800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr10:38384600-38386800	Strong transcription	Fetal Lung	lung
50	chr10:38384600-38387800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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