Variant report

Variant	rs200924
Chromosome Location	chr10:38126170-38126171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:38125960..38130211-chr10:38145750..38148095,4	MCF-7	breast:
2	chr10:38123782..38128970-chr10:38145175..38149505,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236514	Chromatin interaction
ENSG00000198105	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1022698	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10764147	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10827835	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10827836	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11011343	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11011351	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11011407	0.90[AMR][1000 genomes]
rs1208592	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1208681	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1208684	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1208689	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1208708	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1208767	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12774732	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13503	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1735577	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1779017	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1814077	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs200903	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200910	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200935	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs200936	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200937	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200939	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs200943	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2144849	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2180408	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2257186	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2472150	0.80[AMR][1000 genomes]
rs2504130	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2504155	0.81[AMR][1000 genomes]
rs2505232	0.82[AMR][1000 genomes]
rs289648	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs289649	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3851078	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4934906	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4934907	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4934912	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4934916	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs527163	0.82[AMR][1000 genomes]
rs619739	0.81[AMR][1000 genomes]
rs623149	0.81[AMR][1000 genomes]
rs623454	0.81[AMR][1000 genomes]
rs629577	0.82[AMR][1000 genomes]
rs639479	0.82[AMR][1000 genomes]
rs640774	0.81[AMR][1000 genomes]
rs645064	0.82[AMR][1000 genomes]
rs662945	0.83[AMR][1000 genomes]
rs7069702	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7099777	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs719569	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9417256	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs200924	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs200924	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38114000-38128800	ZNF genes & repeats	Liver	Liver
2	chr10:38114400-38130000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
3	chr10:38115600-38129000	ZNF genes & repeats	A549	lung
4	chr10:38115600-38138200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:38115800-38132200	ZNF genes & repeats	Fetal Brain Female	brain
6	chr10:38116000-38128800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:38116200-38127600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr10:38116200-38137800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:38116400-38128400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr10:38116600-38135800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr10:38117200-38127400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
12	chr10:38117200-38129600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:38117400-38129600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:38117400-38131600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr10:38117600-38128800	ZNF genes & repeats	Fetal Lung	lung
16	chr10:38120600-38126400	ZNF genes & repeats	Fetal Intestine Large	intestine
17	chr10:38121200-38127000	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr10:38121200-38127400	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr10:38121200-38128200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr10:38121200-38131200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr10:38121600-38127000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:38121600-38127600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:38121600-38127600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr10:38121600-38128200	Strong transcription	Brain Substantia Nigra	brain
25	chr10:38121800-38127400	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr10:38121800-38129400	Strong transcription	HSMM	muscle
27	chr10:38122000-38127000	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr10:38122200-38128000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:38122200-38128600	Weak transcription	HUVEC	blood vessel
30	chr10:38122200-38134400	Weak transcription	Hela-S3	cervix
31	chr10:38122400-38127200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:38122400-38127200	Strong transcription	Brain Hippocampus Middle	brain
33	chr10:38122600-38126200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:38122600-38127400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr10:38122800-38126400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:38122800-38127000	Strong transcription	Colon Smooth Muscle	Colon
37	chr10:38122800-38127600	Strong transcription	Adipose Nuclei	Adipose
38	chr10:38123000-38128000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:38123000-38144400	Weak transcription	NHEK	skin
40	chr10:38123400-38126400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:38123400-38127000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:38123400-38127200	Strong transcription	Osteobl	bone
43	chr10:38123600-38127600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:38123600-38127800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr10:38123600-38128200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr10:38123600-38128400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr10:38123800-38128200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr10:38123800-38129200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr10:38123800-38129400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr10:38124000-38126400	Strong transcription	Primary B cells from cord blood	blood

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