Variant report

Variant	rs6717670
Chromosome Location	chr2:38948022-38948023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38890666..38892556-chr2:38947054..38950004,2	K562	blood:
2	chr2:38827236..38831286-chr2:38946528..38952512,8	K562	blood:
3	chr2:38938428..38940592-chr2:38945131..38949430,3	K562	blood:
4	chr2:38807837..38810352-chr2:38947655..38950217,2	K562	blood:
5	chr2:38805216..38808046-chr2:38947623..38949999,2	K562	blood:
6	chr2:38822529..38824278-chr2:38946523..38948124,2	K562	blood:

Variant related genes	Relation type
ENSG00000143889	Chromatin interaction
ENSG00000235586	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1010859	0.88[JPT][hapmap]
rs10197412	0.91[CHB][hapmap]
rs10865143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11898812	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618118	1.00[CHB][hapmap]
rs12621103	0.90[CHB][hapmap]
rs13024811	0.91[CHB][hapmap]
rs1529625	0.91[CHB][hapmap]
rs1979143	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2037875	0.91[CHB][hapmap]
rs3097713	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3097714	0.91[CEU][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3097716	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099968	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs3099971	0.82[ASN][1000 genomes]
rs3099990	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3100000	1.00[JPT][hapmap]
rs3108666	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112142	0.81[CHB][hapmap];0.95[MEX][hapmap]
rs3112152	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112156	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112159	0.88[JPT][hapmap]
rs3112161	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112163	1.00[JPT][hapmap]
rs3112178	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3112183	1.00[CHB][hapmap]
rs3112184	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs3112186	0.82[ASN][1000 genomes]
rs3112188	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs3112189	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3112191	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3112192	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3112196	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3134628	0.83[CHB][hapmap]
rs3134637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs35682042	0.80[ASN][1000 genomes]
rs3731838	0.91[CHB][hapmap]
rs55893071	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62142659	0.81[AMR][1000 genomes]
rs62144780	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6715866	0.91[CHB][hapmap]
rs6746818	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1800555	chr2:38929745-38950126	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1830359	chr2:38929745-38950126	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6717670	DHX57	cis	multi-tissue	Pritchard
rs6717670	MORN2	cis	parietal	SCAN
rs6717670	ITGB1	trans	parietal	SCAN
rs6717670	DHX57	cis	cerebellum	SCAN
rs6717670	GALM	cis	parietal	SCAN

Chromatin state (count:104 , 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	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:38918000-38949400	Weak transcription	Primary B cells from cord blood	blood
5	chr2:38918600-38956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:38927600-38957000	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:38928800-38971600	Weak transcription	Small Intestine	intestine
8	chr2:38930000-38956600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:38930600-38965000	Weak transcription	Gastric	stomach
10	chr2:38931200-38948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:38932800-38956800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:38936400-38957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:38936400-38960600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:38936400-38968400	Weak transcription	Colonic Mucosa	Colon
15	chr2:38937200-38956600	Weak transcription	Fetal Brain Female	brain
16	chr2:38937600-38970400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:38938000-38949400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:38938000-38949400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:38938400-38948600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:38939000-38956600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:38939200-38949400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:38939200-38949400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:38939200-38958600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:38940400-38949400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:38943600-38949200	Weak transcription	Liver	Liver
26	chr2:38943600-38949400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:38943600-38949400	Weak transcription	Psoas Muscle	Psoas
28	chr2:38943600-38956000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:38943600-38958600	Weak transcription	Aorta	Aorta
30	chr2:38943800-38948800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:38944000-38949400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:38945200-38948200	Weak transcription	Primary T cells from cord blood	blood
33	chr2:38945800-38949000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:38946200-38949000	Enhancers	HMEC	breast
35	chr2:38946400-38948200	Enhancers	Left Ventricle	heart
36	chr2:38946400-38948600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:38946400-38949000	Weak transcription	Thymus	Thymus
38	chr2:38946400-38957000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:38946600-38948800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:38946800-38948200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:38946800-38948200	Enhancers	Right Atrium	heart
42	chr2:38946800-38949200	Enhancers	NHLF	lung
43	chr2:38947000-38948200	Enhancers	Lung	lung
44	chr2:38947000-38948600	Enhancers	NH-A	brain
45	chr2:38947000-38948800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:38947000-38948800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:38947000-38948800	Enhancers	Fetal Lung	lung
48	chr2:38947000-38951000	Enhancers	Fetal Heart	heart
49	chr2:38947200-38948200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:38947200-38948200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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