Variant report

Variant	rs7519860
Chromosome Location	chr1:114482520-114482521
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114480724..114483569-chr1:114488715..114491848,4	K562	blood:
2	chr1:114353357..114355153-chr1:114481676..114484296,2	K562	blood:
3	chr1:114480724..114484665-chr1:114488445..114490479,3	K562	blood:

Variant related genes	Relation type
ENSG00000231128	Chromatin interaction
ENSG00000081019	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10108	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10494162	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10494163	0.88[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.81[EUR][1000 genomes]
rs11102703	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102706	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102707	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11102708	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11102709	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12060750	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12125546	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12127377	0.94[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12129050	0.94[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1217444	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1503832	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1553449	0.99[ASN][1000 genomes]
rs1553450	0.94[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17852555	0.88[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1910485	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1985435	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985436	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41302825	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6537800	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6669370	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674384	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7364	0.92[CHD][hapmap];0.85[JPT][hapmap]
rs7545300	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7546851	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs756493	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs878129	0.83[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7519860	DCLRE1B	cis	normal skin	skin_eQTL
rs7519860	DCLRE1B	cis	multi-tissue	Pritchard
rs7519860	PTPN22	cis	parietal	SCAN
rs7519860	DENND2C	cis	cerebellum	SCAN
rs7519860	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs7519860	DCLRE1B	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114473400-114483000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:114473400-114483200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:114473600-114483000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:114473600-114483000	Weak transcription	Placenta	Placenta
5	chr1:114473600-114483200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:114473600-114499200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:114473800-114483000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:114473800-114483000	Weak transcription	Colonic Mucosa	Colon
9	chr1:114473800-114483200	Weak transcription	Right Ventricle	heart
10	chr1:114474200-114482600	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:114474200-114483000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:114474200-114483000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:114474200-114483200	Weak transcription	Aorta	Aorta
14	chr1:114474200-114483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:114474200-114489600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:114474400-114483200	Weak transcription	Fetal Brain Female	brain
17	chr1:114474600-114483200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:114474600-114483200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr1:114474800-114482600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:114474800-114482800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:114474800-114483000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:114474800-114483000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:114474800-114483000	Weak transcription	Fetal Intestine Large	intestine
24	chr1:114474800-114483400	Weak transcription	HMEC	breast
25	chr1:114474800-114483400	Weak transcription	HSMMtube	muscle
26	chr1:114474800-114483800	Weak transcription	Fetal Kidney	kidney
27	chr1:114474800-114483800	Weak transcription	NHDF-Ad	bronchial
28	chr1:114474800-114488600	Weak transcription	Stomach Mucosa	stomach
29	chr1:114475000-114483000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:114475000-114483000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:114475000-114483000	Weak transcription	Brain Germinal Matrix	brain
32	chr1:114475000-114483200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:114475000-114483200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:114475000-114483400	Weak transcription	NH-A	brain
35	chr1:114475200-114482800	Weak transcription	Osteobl	bone
36	chr1:114475200-114483000	Weak transcription	Fetal Intestine Small	intestine
37	chr1:114475200-114483200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:114475200-114483200	Weak transcription	HSMM	muscle
39	chr1:114475400-114485600	Weak transcription	Fetal Brain Male	brain
40	chr1:114475400-114485600	Weak transcription	A549	lung
41	chr1:114475600-114483000	Enhancers	Primary T cells fromperipheralblood	blood
42	chr1:114475600-114483200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:114475800-114483000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:114476000-114482600	Weak transcription	Brain Substantia Nigra	brain
45	chr1:114476000-114483000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr1:114476000-114483200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:114476200-114482600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:114476200-114483000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:114476400-114482600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:114476600-114483000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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