Variant report

Variant	rs2804649
Chromosome Location	chr10:38737254-38737255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr10:38737072-38737492	K562	blood:	n/a	chr10:38737453-38737462 chr10:38737449-38737462 chr10:38737447-38737465 chr10:38737450-38737460 chr10:38737191-38737209 chr10:38737442-38737463
2	CTCF	chr10:38737005-38737607	K562	blood:	n/a	chr10:38737453-38737462 chr10:38737449-38737462 chr10:38737447-38737465 chr10:38737450-38737460 chr10:38737191-38737209 chr10:38737508-38737521 chr10:38737442-38737463
3	CTCF	chr10:38736997-38737458	K562	blood:	n/a	chr10:38737191-38737209
4	CTCF	chr10:38737180-38737330	WERI-Rb-1	eye:	n/a	chr10:38737191-38737209

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF37A-3	chr10:38736592-38737700	ENSG00000225119.2

Variant related genes	Relation type
ENSG00000203496	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1892144	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs2145672	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs2754353	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs2754360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2754361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2754495	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs2800485	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap]
rs2804641	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs2804675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427860	chr10:38588021-38818835	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv895034	chr10:38632352-38743545	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2764202	chr10:38641508-39076221	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1048953	chr10:38645824-39074038	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv428230	chr10:38652001-38818835	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2757379	chr10:38677023-38978680	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2759744	chr10:38677023-39154935	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv947860	chr10:38678275-38747483	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv895035	chr10:38678941-38739427	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv895036	chr10:38678941-38741100	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv895037	chr10:38678941-38741777	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv895038	chr10:38678941-38890240	ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1036840	chr10:38682579-39074038	ZNF genes & repeats Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv540569	chr10:38689167-38769822	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
15	esv16395	chr10:38693709-38772324	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv821215	chr10:38693709-38772324	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv540571	chr10:38696654-38743406	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv540572	chr10:38696654-38769822	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv1052697	chr10:38696664-39030136	Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
20	nsv1043781	chr10:38696664-39074038	ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv895039	chr10:38700234-38739557	Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv895040	chr10:38700234-38741100	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv895041	chr10:38700234-38741777	Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv550420	chr10:38700234-38768341	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv895042	chr10:38700234-38775205	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv895043	chr10:38700234-38790428	Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv948261	chr10:38720728-38744526	Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
28	nsv895044	chr10:38725007-38741100	Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
29	nsv895045	chr10:38725007-38741777	Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
30	esv2762857	chr10:38733507-39076221	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2804649	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2804649	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38692200-38741000	Weak transcription	Aorta	Aorta
2	chr10:38692400-38739600	Weak transcription	Gastric	stomach
3	chr10:38692800-38737400	Weak transcription	Fetal Intestine Large	intestine
4	chr10:38692800-38737600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:38692800-38741200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr10:38693000-38737400	Weak transcription	Placenta	Placenta
7	chr10:38693000-38739200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr10:38698600-38738800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr10:38700200-38739600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr10:38707600-38738800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr10:38710400-38737400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr10:38711200-38739600	Weak transcription	Adipose Nuclei	Adipose
13	chr10:38715800-38737400	Weak transcription	Fetal Brain Female	brain
14	chr10:38723400-38739400	Weak transcription	Brain Angular Gyrus	brain
15	chr10:38724600-38737400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:38724800-38739600	Weak transcription	Fetal Lung	lung
17	chr10:38725000-38739000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:38725400-38739000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:38726400-38739400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:38727800-38740600	Weak transcription	Psoas Muscle	Psoas
21	chr10:38731400-38739200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr10:38733400-38739600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr10:38733800-38739200	Weak transcription	Dnd41	blood
24	chr10:38734000-38737400	Weak transcription	Brain Germinal Matrix	brain
25	chr10:38734400-38740000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:38735200-38737400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:38735400-38739600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr10:38735800-38737400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr10:38735800-38737400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr10:38736200-38738600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr10:38736600-38738400	Strong transcription	Liver	Liver
32	chr10:38736600-38738800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr10:38736600-38739200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr10:38736800-38737600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:38736800-38737800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr10:38736800-38738000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:38736800-38738000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr10:38736800-38738200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr10:38736800-38738400	Strong transcription	Brain Anterior Caudate	brain
40	chr10:38736800-38738400	Strong transcription	Fetal Intestine Small	intestine
41	chr10:38736800-38738400	Strong transcription	Ovary	ovary
42	chr10:38736800-38738400	Strong transcription	Right Ventricle	heart
43	chr10:38736800-38738400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr10:38736800-38738600	Strong transcription	Pancreas	Pancrea
45	chr10:38736800-38738800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr10:38736800-38738800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr10:38736800-38738800	Strong transcription	Thymus	Thymus
48	chr10:38736800-38739000	Strong transcription	Lung	lung
49	chr10:38736800-38740600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr10:38737000-38737600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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