Variant report

Variant	rs16996019
Chromosome Location	chr4:76644744-76644745
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76640891..76645674-chr4:76646043..76650611,7	K562	blood:
2	chr4:76634356..76637293-chr4:76642059..76644795,2	MCF-7	breast:
3	chr4:76597399..76599745-chr4:76643717..76646683,2	MCF-7	breast:
4	chr4:76640057..76642615-chr4:76643666..76645521,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138757	Chromatin interaction
ENSG00000138768	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10028291	0.80[YRI][hapmap]
rs10031352	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10856853	0.92[JPT][hapmap]
rs11097112	0.80[YRI][hapmap]
rs11097117	0.82[ASN][1000 genomes]
rs11097121	0.82[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs11556146	0.92[JPT][hapmap]
rs11723767	0.84[JPT][hapmap]
rs11727895	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11732850	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11734358	0.86[ASN][1000 genomes]
rs11935073	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs12233780	0.82[ASN][1000 genomes]
rs12498415	0.92[JPT][hapmap]
rs12505147	0.84[ASN][1000 genomes]
rs12506101	0.84[ASN][1000 genomes]
rs12508200	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12508992	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12511212	0.82[ASN][1000 genomes]
rs12511575	0.92[JPT][hapmap]
rs13133144	0.80[YRI][hapmap]
rs13137229	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13145290	0.80[YRI][hapmap]
rs17000786	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17000794	0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs17000864	0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs186563	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2089253	0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs2175640	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271472	0.80[YRI][hapmap]
rs28573275	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28680723	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324686	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324688	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324690	0.87[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324691	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324693	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324696	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324697	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324698	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324700	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324701	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324703	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324709	0.91[CEU][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs324712	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324713	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324714	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap]
rs324719	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324722	0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324723	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324726	0.91[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs324727	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324730	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324731	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs324733	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324735	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs324738	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs324740	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4262008	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4610362	0.92[JPT][hapmap]
rs4859408	0.80[YRI][hapmap]
rs61603278	0.82[ASN][1000 genomes]
rs6531816	0.92[JPT][hapmap]
rs6531901	0.80[YRI][hapmap]
rs6531934	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs6827016	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6834747	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6856162	0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs72858061	0.82[ASN][1000 genomes]
rs7657198	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7663617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7684778	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693127	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16996019	USO1	cis	parietal	SCAN
rs16996019	DLK2	trans	cerebellum	SCAN
rs16996019	FAM47E	cis	parietal	SCAN
rs16996019	SCARB2	cis	cerebellum	SCAN
rs16996019	CDKL2	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76599600-76647600	Weak transcription	Fetal Brain Female	brain
2	chr4:76623800-76647600	Weak transcription	Fetal Heart	heart
3	chr4:76624400-76647200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:76624400-76647800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:76624600-76646800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr4:76624800-76647600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr4:76631000-76648800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:76631600-76648000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:76633600-76647000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:76633600-76648200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:76633800-76648000	Weak transcription	Fetal Kidney	kidney
12	chr4:76634000-76647800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:76634000-76647800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:76635200-76644800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:76635400-76648200	Weak transcription	Primary B cells from cord blood	blood
16	chr4:76636400-76648600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:76640400-76648200	Weak transcription	Stomach Mucosa	stomach
18	chr4:76640800-76647200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:76640800-76647200	Weak transcription	Fetal Lung	lung
20	chr4:76640800-76647600	Weak transcription	Fetal Thymus	thymus
21	chr4:76640800-76648200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:76640800-76648200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:76640800-76648400	Weak transcription	Placenta	Placenta
24	chr4:76640800-76648400	Weak transcription	Right Atrium	heart
25	chr4:76640800-76649200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:76640800-76649400	Weak transcription	Lung	lung
27	chr4:76641000-76645000	Weak transcription	GM12878-XiMat	blood
28	chr4:76641000-76647000	Weak transcription	A549	lung
29	chr4:76641000-76647400	Weak transcription	Ovary	ovary
30	chr4:76641000-76647600	Weak transcription	Osteobl	bone
31	chr4:76641000-76647800	Weak transcription	Brain Germinal Matrix	brain
32	chr4:76641000-76648000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:76641000-76648200	Weak transcription	Brain Anterior Caudate	brain
34	chr4:76641000-76648200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:76641000-76648200	Weak transcription	Fetal Intestine Small	intestine
36	chr4:76641000-76648200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:76641200-76646800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:76641200-76647200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:76641200-76647400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:76641200-76647600	Weak transcription	NH-A	brain
41	chr4:76641200-76647800	Weak transcription	Brain Angular Gyrus	brain
42	chr4:76641200-76647800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:76641200-76648000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:76641200-76648200	Weak transcription	NHDF-Ad	bronchial
45	chr4:76641400-76646800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:76641400-76647400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:76641400-76647400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:76641400-76647400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:76641400-76647400	Weak transcription	HSMMtube	muscle
50	chr4:76641400-76647400	Weak transcription	NHLF	lung

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