Variant report

Variant	rs2474573
Chromosome Location	chr10:38385441-38385442
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	chr10:38299349..38301423-chr10:38382665..38385531,5	K562	blood:
2	chr10:38298494..38301362-chr10:38382665..38385531,3	K562	blood:

Variant related genes	Relation type
ENSG00000189180	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1138252	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1329786	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13503	0.81[CEU][hapmap];0.86[CHD][hapmap]
rs1548255	1.00[ASW][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap]
rs176838	0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
rs176876	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176877	0.80[ASN][1000 genomes]
rs176879	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176880	1.00[ASW][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap]
rs176882	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176885	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176886	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs176887	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs176889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2008449	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2021649	0.81[ASN][1000 genomes]
rs2021650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2023351	0.80[ASN][1000 genomes]
rs2144859	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2178962	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263162	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263163	0.81[ASN][1000 genomes]
rs2263164	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2384731	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2472150	0.85[CEU][hapmap];0.88[CHD][hapmap]
rs2472173	0.80[ASN][1000 genomes]
rs2472174	0.80[ASN][1000 genomes]
rs2472175	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2472176	0.81[ASN][1000 genomes]
rs2472177	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2472178	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2472179	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2472181	0.81[ASN][1000 genomes]
rs2474554	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474563	0.80[ASN][1000 genomes]
rs2474564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2474565	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2474566	0.81[ASN][1000 genomes]
rs2474567	0.81[ASN][1000 genomes]
rs2474568	1.00[ASW][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2474569	0.81[ASN][1000 genomes]
rs2474570	0.94[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];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474571	0.81[ASN][1000 genomes]
rs2474572	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2474574	0.81[ASN][1000 genomes]
rs2474575	0.81[ASN][1000 genomes]
rs2474579	0.81[ASN][1000 genomes]
rs2474580	0.81[ASN][1000 genomes]
rs2474581	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2474591	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474596	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474597	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474610	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504120	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504121	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504127	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504139	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504140	0.81[ASN][1000 genomes]
rs2504141	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504148	0.81[ASN][1000 genomes]
rs2505179	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505185	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505186	0.81[ASN][1000 genomes]
rs2505187	0.81[ASN][1000 genomes]
rs2505188	0.81[ASN][1000 genomes]
rs2505190	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505191	0.81[ASN][1000 genomes]
rs2505192	0.82[JPT][hapmap]
rs2505193	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2505194	1.00[ASW][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2505195	0.80[ASN][1000 genomes]
rs2505196	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2505197	0.81[ASN][1000 genomes]
rs2505198	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2505202	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs2505203	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2505232	0.83[CEU][hapmap]
rs2505235	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505236	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505244	0.94[ASN][1000 genomes]
rs2505249	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505250	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505251	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505252	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505258	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505259	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2800485	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.89[YRI][hapmap]
rs2983343	0.81[ASN][1000 genomes]
rs496627	0.85[CEU][hapmap];0.86[CHD][hapmap]
rs619739	0.84[CEU][hapmap]
rs626519	0.85[CEU][hapmap];0.86[CHD][hapmap]
rs629577	0.85[CEU][hapmap]
rs645064	0.85[CEU][hapmap];0.88[CHD][hapmap]
rs6482060	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7915062	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9299760	0.80[ASN][1000 genomes]
rs932538	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9418322	0.80[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2474573	HSD17B7P2	cis	Whole Blood	GTEx
rs2474573	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2474573	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2474573	HSD17B7P2	cis	Esophagus Mucosa	GTEx
rs2474573	ZNF37A	cis	lymphoblastoid	seeQTL

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	chr10:38384200-38389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:38384200-38389200	Weak transcription	Aorta	Aorta
6	chr10:38384400-38385600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:38384400-38385800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:38384400-38386000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr10:38384400-38386800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr10:38384400-38388200	Weak transcription	Psoas Muscle	Psoas
11	chr10:38384400-38388800	Weak transcription	Fetal Intestine Small	intestine
12	chr10:38384400-38389200	Weak transcription	Small Intestine	intestine
13	chr10:38384400-38389400	Weak transcription	Thymus	Thymus
14	chr10:38384400-38396400	Weak transcription	HUVEC	blood vessel
15	chr10:38384600-38385600	Enhancers	HepG2	liver
16	chr10:38384600-38386200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:38384600-38386200	Strong transcription	HSMMtube	muscle
18	chr10:38384600-38386600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr10:38384600-38386800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:38384600-38386800	Strong transcription	Fetal Lung	lung
21	chr10:38384600-38387800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr10:38384600-38388000	Strong transcription	Placenta	Placenta
23	chr10:38384600-38388000	Weak transcription	NHLF	lung
24	chr10:38384600-38388200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr10:38384600-38388200	Strong transcription	Fetal Muscle Leg	muscle
26	chr10:38384600-38388600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr10:38384600-38388600	ZNF genes & repeats	A549	lung
28	chr10:38384600-38388600	Strong transcription	NH-A	brain
29	chr10:38384600-38388800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr10:38384600-38389200	Weak transcription	Esophagus	oesophagus
31	chr10:38384600-38390600	Weak transcription	Fetal Heart	heart
32	chr10:38384600-38390800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr10:38384600-38390800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr10:38384600-38391200	Weak transcription	Colonic Mucosa	Colon
35	chr10:38384600-38391400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr10:38384600-38391400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr10:38384600-38391400	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr10:38384600-38391800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:38384600-38392800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr10:38384600-38392800	Weak transcription	Gastric	stomach
41	chr10:38384800-38385600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr10:38384800-38386400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:38384800-38386400	Strong transcription	Fetal Brain Female	brain
44	chr10:38384800-38386600	Strong transcription	Fetal Stomach	stomach
45	chr10:38384800-38386800	Weak transcription	Brain Angular Gyrus	brain
46	chr10:38384800-38387000	Strong transcription	Fetal Intestine Large	intestine
47	chr10:38384800-38387200	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr10:38384800-38387400	Strong transcription	HMEC	breast
49	chr10:38384800-38387600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:38384800-38387600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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