Variant report

Variant	rs1979143
Chromosome Location	chr2:39041464-39041465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:38976507..38979814-chr2:39040782..39043976,4	K562	blood:
2	chr2:38977117..38979814-chr2:39041062..39044349,4	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1010859	0.83[ASW][hapmap];0.88[JPT][hapmap]
rs10197412	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs10865143	0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11124646	0.88[CEU][hapmap]
rs11898812	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs12468732	0.84[EUR][1000 genomes]
rs12618118	0.90[CHB][hapmap]
rs12621103	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.82[ASN][1000 genomes]
rs13024811	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap]
rs1529625	0.82[CHB][hapmap]
rs2037875	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs3097713	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs3097714	1.00[CEU][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs3099961	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099965	0.92[ASN][1000 genomes]
rs3099968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099971	0.89[ASN][1000 genomes]
rs3099975	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099977	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099980	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099990	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099992	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3100000	1.00[JPT][hapmap]
rs3112142	0.83[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112143	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3112150	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112159	0.83[ASW][hapmap];0.88[JPT][hapmap]
rs3112163	0.83[ASW][hapmap];1.00[JPT][hapmap]
rs3112178	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs3112183	0.80[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap]
rs3112184	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs3112186	0.89[ASN][1000 genomes]
rs3112188	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs3112189	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3112191	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3112192	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3112194	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112196	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs3112198	0.88[ASN][1000 genomes]
rs3112204	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112209	0.85[AMR][1000 genomes]
rs3112215	0.84[CEU][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3134628	0.82[CHD][hapmap]
rs3134637	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs35387882	0.84[ASN][1000 genomes]
rs3731838	0.82[CHB][hapmap]
rs4670268	0.86[JPT][hapmap]
rs6544175	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6715866	0.82[CHB][hapmap];0.89[CHD][hapmap]
rs6717670	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6746818	0.82[CHB][hapmap]
rs756338	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1979143	DHX57	cis	cerebellum	SCAN
rs1979143	GALM	cis	parietal	SCAN
rs1979143	ITGB1	trans	parietal	SCAN
rs1979143	MORN2	cis	parietal	SCAN
rs1979143	DHX57	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:39009200-39042600	Weak transcription	Fetal Kidney	kidney
4	chr2:39009200-39050000	Weak transcription	HMEC	breast
5	chr2:39009200-39052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:39017600-39042200	Weak transcription	Small Intestine	intestine
7	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:39022000-39042600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
10	chr2:39024000-39053000	Weak transcription	Psoas Muscle	Psoas
11	chr2:39025600-39042400	Weak transcription	Hela-S3	cervix
12	chr2:39025600-39042400	Weak transcription	HSMM	muscle
13	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
15	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:39033000-39053000	Weak transcription	Fetal Brain Male	brain
17	chr2:39033800-39050200	Weak transcription	K562	blood
18	chr2:39036000-39046800	Strong transcription	Fetal Stomach	stomach
19	chr2:39036000-39054000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:39036200-39043800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:39036400-39051600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:39037000-39046000	Strong transcription	Fetal Intestine Small	intestine
23	chr2:39037000-39046800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:39037200-39055800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:39037400-39041600	Strong transcription	Placenta	Placenta
26	chr2:39037400-39043200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:39037400-39046000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:39037400-39046600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:39037400-39046600	Strong transcription	Fetal Brain Female	brain
30	chr2:39037400-39046800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr2:39037400-39047200	Strong transcription	Primary T cells from cord blood	blood
32	chr2:39037400-39047800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:39037400-39047800	Strong transcription	Left Ventricle	heart
34	chr2:39037400-39052000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:39037400-39054000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:39037400-39054000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:39037400-39054600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:39037600-39043000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr2:39037600-39043200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr2:39037600-39043400	Strong transcription	Primary B cells from cord blood	blood
41	chr2:39037600-39046200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:39037600-39046600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:39037600-39046600	Strong transcription	Fetal Thymus	thymus
44	chr2:39037600-39046800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:39037600-39046800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:39037600-39047200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:39037600-39048800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:39037800-39053800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:39038000-39044800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:39038200-39056000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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