Variant report

Variant	rs1997377
Chromosome Location	chr2:38951666-38951667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38824669..38828895-chr2:38950792..38955552,5	K562	blood:
2	chr2:38950132..38952151-chr2:38956554..38959124,2	MCF-7	breast:
3	chr2:38892250..38893779-chr2:38950404..38953319,2	MCF-7	breast:
4	chr2:38824718..38826820-chr2:38951264..38953232,2	K562	blood:
5	chr2:38827236..38831286-chr2:38946528..38952512,8	K562	blood:
6	chr2:38948167..38950183-chr2:38951156..38954719,3	MCF-7	breast:
7	chr2:38782788..38784491-chr2:38951489..38953190,2	K562	blood:
8	chr2:38949315..38952552-chr2:38977196..38979499,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000235586	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10173118	0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[MEX][hapmap]
rs10176932	0.81[CHB][hapmap]
rs10197412	0.87[MEX][hapmap]
rs10865143	0.83[MEX][hapmap]
rs11124645	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11124646	0.94[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1138974	0.85[ASN][1000 genomes]
rs11694383	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs12712614	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712621	0.80[CHB][hapmap]
rs13011311	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13029406	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs13383541	0.81[CHB][hapmap]
rs1529625	0.92[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1530852	0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs1530853	0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs17494049	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1965751	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1968411	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1979142	0.81[CHB][hapmap]
rs2037875	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2043188	0.81[CHB][hapmap]
rs2272445	0.94[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2373473	0.90[JPT][hapmap]
rs3099940	0.90[JPT][hapmap]
rs3099941	0.90[JPT][hapmap]
rs3099943	0.81[JPT][hapmap]
rs3099945	0.81[JPT][hapmap]
rs3112200	0.88[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs3112215	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs35182980	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35682042	0.85[AMR][1000 genomes]
rs3731838	0.82[MEX][hapmap]
rs3770681	0.81[CHB][hapmap]
rs4602206	0.88[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs4630748	0.83[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs4670891	0.88[ASN][1000 genomes]
rs6544173	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6715866	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs6728394	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6731386	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6736004	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6756847	0.94[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7419616	0.81[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap]
rs7419838	0.81[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs7581263	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7581653	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7589162	0.81[CHB][hapmap]
rs7596239	0.89[ASN][1000 genomes]
rs7603676	0.88[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7603821	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7604054	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7604132	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1797820	chr2:38941956-38972456	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv820974	chr2:38945458-38972971	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv1814150	chr2:38948483-38972456	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv1795154	chr2:38951608-38971432	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
7	esv1800732	chr2:38951608-38973837	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1997377	DHX57	cis	cerebellum	SCAN
rs1997377	MORN2	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
2	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:38918600-38956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:38927600-38957000	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:38928800-38971600	Weak transcription	Small Intestine	intestine
6	chr2:38930000-38956600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:38930600-38965000	Weak transcription	Gastric	stomach
8	chr2:38932800-38956800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:38936400-38957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:38936400-38960600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:38936400-38968400	Weak transcription	Colonic Mucosa	Colon
12	chr2:38937200-38956600	Weak transcription	Fetal Brain Female	brain
13	chr2:38937600-38970400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:38939000-38956600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:38939200-38958600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:38943600-38956000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:38943600-38958600	Weak transcription	Aorta	Aorta
18	chr2:38946400-38957000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:38947800-38953200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr2:38948000-38952400	Weak transcription	HepG2	liver
21	chr2:38948000-38953400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:38948000-38955800	Weak transcription	Fetal Intestine Large	intestine
23	chr2:38948000-38958600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:38948200-38956600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:38948200-38956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:38948200-38956600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:38948200-38957000	Weak transcription	Spleen	Spleen
28	chr2:38948200-38958600	Weak transcription	Esophagus	oesophagus
29	chr2:38948200-38968200	Weak transcription	Stomach Mucosa	stomach
30	chr2:38948400-38952800	Weak transcription	K562	blood
31	chr2:38948400-38956600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:38948400-38958600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:38948400-38958800	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:38948400-38964400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:38948400-38964600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:38948400-38970600	Weak transcription	NHEK	skin
37	chr2:38948600-38956600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:38948600-38956800	Weak transcription	Brain Anterior Caudate	brain
39	chr2:38948600-38957000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:38948600-38959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:38948600-38970200	Weak transcription	NHDF-Ad	bronchial
42	chr2:38948600-38971200	Weak transcription	Fetal Kidney	kidney
43	chr2:38948800-38956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:38948800-38956600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:38948800-38956800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:38948800-38957000	Weak transcription	Lung	lung
47	chr2:38948800-38960200	Weak transcription	Hela-S3	cervix
48	chr2:38948800-38960600	Weak transcription	Brain Angular Gyrus	brain
49	chr2:38948800-38964600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:38949000-38956800	Weak transcription	Ovary	ovary

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