Variant report

Variant	rs2180408
Chromosome Location	chr10:38262957-38262958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:38259253..38262996-chr10:38263310..38267039,6	K562	blood:
2	chr10:38259972..38262961-chr10:38264672..38266951,4	K562	blood:
3	chr10:38260688..38263129-chr10:38263289..38264919,2	MCF-7	breast:
4	chr10:38262821..38267029-chr10:38297888..38300843,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175395	Chromatin interaction
ENSG00000189180	Chromatin interaction
ENSG00000226447	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10764147	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10827835	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10827836	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11011407	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1208559	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1208592	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1208681	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1208684	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1208689	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13503	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1735577	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs200903	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200910	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200924	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200935	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs200936	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200937	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200939	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200943	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2144849	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2257186	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2472150	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2504130	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504155	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505232	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851078	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4934916	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs496627	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527163	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs619739	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs623149	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs623454	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs626519	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs629577	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs639479	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs640774	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs645064	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs662945	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7069702	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7099777	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs719569	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1052703	chr10:38174640-38266472	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2180408	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2180408	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38239600-38264400	Weak transcription	Fetal Heart	heart
2	chr10:38239600-38264600	Weak transcription	Stomach Mucosa	stomach
3	chr10:38240800-38264000	Weak transcription	NHLF	lung
4	chr10:38241800-38264400	Weak transcription	NHEK	skin
5	chr10:38242600-38264400	Weak transcription	HUVEC	blood vessel
6	chr10:38246400-38264000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr10:38246400-38264400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:38247000-38263000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr10:38253800-38263600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:38254000-38263800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr10:38254200-38264000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:38254200-38264200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr10:38254200-38264400	Weak transcription	NH-A	brain
14	chr10:38254200-38264600	Weak transcription	Gastric	stomach
15	chr10:38254200-38264600	Weak transcription	Pancreas	Pancrea
16	chr10:38254400-38263600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr10:38254400-38263600	Weak transcription	Brain Angular Gyrus	brain
18	chr10:38254400-38264400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:38254400-38264400	Weak transcription	Aorta	Aorta
20	chr10:38254600-38263600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr10:38254600-38263800	Weak transcription	Colon Smooth Muscle	Colon
22	chr10:38254600-38263800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr10:38254600-38264200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr10:38254800-38264600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr10:38255600-38264600	Weak transcription	Spleen	Spleen
26	chr10:38256000-38263800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr10:38256400-38264200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr10:38256600-38263800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr10:38256600-38263800	Weak transcription	Dnd41	blood
30	chr10:38256600-38264600	Weak transcription	Lung	lung
31	chr10:38256800-38264600	Weak transcription	Placenta	Placenta
32	chr10:38256800-38264600	Weak transcription	Right Ventricle	heart
33	chr10:38257200-38264400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:38257400-38264400	Weak transcription	Fetal Intestine Small	intestine
35	chr10:38257400-38265000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr10:38258000-38264400	Weak transcription	HSMMtube	muscle
37	chr10:38258200-38264200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr10:38258600-38263800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr10:38258600-38264200	Weak transcription	A549	lung
40	chr10:38258600-38264400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr10:38258600-38264400	Weak transcription	Osteobl	bone
42	chr10:38258600-38264600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr10:38258600-38264600	Weak transcription	Ovary	ovary
44	chr10:38259000-38264000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr10:38259000-38264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr10:38259200-38264000	Weak transcription	Liver	Liver
47	chr10:38259400-38263000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr10:38259400-38264400	Weak transcription	Fetal Intestine Large	intestine
49	chr10:38259400-38264400	Weak transcription	HSMM	muscle
50	chr10:38259800-38263400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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