Variant report

Variant	rs12136083
Chromosome Location	chr1:63163073-63163074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:63152195..63155380-chr1:63161235..63164349,3	K562	blood:
2	chr1:63151912..63156193-chr1:63162358..63164958,4	K562	blood:

Variant related genes	Relation type
ENSG00000116641	Chromatin interaction
ENSG00000235545	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1002687	0.91[CEU][hapmap]
rs10157265	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10159255	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10789113	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10789117	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10789118	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10789119	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10789120	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10889333	0.80[EUR][1000 genomes]
rs10889337	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs10889338	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10889343	0.87[EUR][1000 genomes]
rs10889344	0.87[EUR][1000 genomes]
rs10889347	0.91[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10889348	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10889349	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs10889350	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10889352	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10889353	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10889354	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10889356	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10889357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889360	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889364	0.84[ASN][1000 genomes]
rs11207977	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11207980	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11207981	0.95[CEU][hapmap]
rs11207982	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11207990	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs11207992	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207994	0.87[AMR][1000 genomes]
rs11207995	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207996	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207997	0.83[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11207998	1.00[JPT][hapmap]
rs11207999	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11208000	0.85[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11208001	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11208004	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11208007	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11485618	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11577840	0.91[CEU][hapmap]
rs1168013	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs1168018	0.91[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs1168022	0.90[CEU][hapmap]
rs1168023	0.91[CEU][hapmap]
rs1168026	0.91[CEU][hapmap]
rs1168030	0.91[CEU][hapmap]
rs1168031	0.91[CEU][hapmap]
rs1168032	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs1168042	0.91[CEU][hapmap]
rs1168045	0.91[CEU][hapmap];0.97[TSI][hapmap]
rs1168085	0.90[EUR][1000 genomes]
rs1168086	0.95[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168089	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168093	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168097	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168098	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168099	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168102	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168103	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168107	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168113	0.96[CEU][hapmap];0.90[CHD][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1168114	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168124	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168128	0.82[EUR][1000 genomes]
rs1168132	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1184865	0.91[CEU][hapmap];0.97[TSI][hapmap]
rs12023282	0.84[ASN][1000 genomes]
rs12024044	0.84[ASN][1000 genomes]
rs12025111	0.82[ASN][1000 genomes]
rs12025800	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12026283	0.84[ASN][1000 genomes]
rs12027341	0.84[ASN][1000 genomes]
rs12028944	0.84[ASN][1000 genomes]
rs12029452	0.84[ASN][1000 genomes]
rs12031537	0.89[ASN][1000 genomes]
rs12038768	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12039115	1.00[JPT][hapmap]
rs12041843	0.90[ASN][1000 genomes]
rs12042319	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12043910	0.89[ASN][1000 genomes]
rs12047226	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12048208	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12049254	0.84[ASN][1000 genomes]
rs12090886	1.00[CEU][hapmap]
rs12116574	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12239736	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12239737	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1472257	0.87[EUR][1000 genomes]
rs1570694	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1627591	0.91[CEU][hapmap]
rs1629122	0.86[EUR][1000 genomes]
rs1748195	0.91[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1748197	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1748199	0.91[CEU][hapmap];0.93[CHD][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1748200	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs1748201	0.91[CEU][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1781195	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs1781212	0.91[CEU][hapmap]
rs1781221	0.91[CEU][hapmap]
rs2029763	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2131925	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2131926	0.87[EUR][1000 genomes]
rs2366636	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2366638	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2479464	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28399032	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34152715	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3850634	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4329540	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs4344355	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4409689	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4459145	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4495740	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4587594	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61471917	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61775910	0.81[AMR][1000 genomes]
rs6587980	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6657050	0.81[AMR][1000 genomes]
rs6666816	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6675401	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6678483	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6682423	0.96[CEU][hapmap];0.90[CHD][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6686331	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6690733	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6693353	0.84[EUR][1000 genomes]
rs6696502	0.87[EUR][1000 genomes]
rs746735	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7518497	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519785	0.86[EUR][1000 genomes]
rs7520810	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7531579	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539035	0.91[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7555577	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs880694	0.96[CEU][hapmap];0.90[CHD][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9787151	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9787156	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs993013	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs995000	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][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	nsv1014376	chr1:62976472-63181359	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12136083	DOCK7	cis	uninvolved skin	skin_eQTL
rs12136083	DOCK7	cis	lesional skin	skin_eQTL
rs12136083	DOCK7	cis	lymphoblastoid	seeQTL
rs12136083	RAB11FIP2	trans	parietal	SCAN
rs12136083	DOCK7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63155800-63165000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:63156400-63170400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:63156600-63170400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:63157400-63170400	Weak transcription	Fetal Stomach	stomach
5	chr1:63157600-63173000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:63157600-63180800	Weak transcription	Fetal Brain Male	brain
7	chr1:63157800-63167200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:63158200-63164200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:63158400-63166800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:63158800-63170600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:63159600-63166000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:63160400-63171000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:63160600-63166000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:63160600-63170400	Weak transcription	Fetal Intestine Small	intestine
15	chr1:63160600-63170600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:63162200-63163600	Enhancers	HepG2	liver

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