Variant report

Variant	rs4853684
Chromosome Location	chr2:191062951-191062952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:191058197..191060868-chr2:191061375..191063080,2	K562	blood:
2	chr2:191058046..191059738-chr2:191062571..191064131,2	MCF-7	breast:
3	chr2:191062034..191064478-chr2:191069746..191072608,2	K562	blood:

Variant related genes	Relation type
ENSG00000198130	Chromatin interaction

Extended variants
information (count: 200 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:198)

rs_ID	r²[population]
rs10173593	0.86[EUR][1000 genomes]
rs10183133	0.89[EUR][1000 genomes]
rs10188044	0.87[EUR][1000 genomes]
rs10191068	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs10196013	0.87[EUR][1000 genomes]
rs10196351	0.86[EUR][1000 genomes]
rs10200496	0.87[EUR][1000 genomes]
rs10209516	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs10209984	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs1058180	0.81[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1058227	0.87[EUR][1000 genomes]
rs1058230	0.87[EUR][1000 genomes]
rs10931448	0.82[EUR][1000 genomes]
rs10931450	0.84[MEX][hapmap];0.92[TSI][hapmap]
rs1114863	0.83[EUR][1000 genomes]
rs11216	0.90[EUR][1000 genomes]
rs11542	0.87[EUR][1000 genomes]
rs11683636	0.95[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11683763	0.87[EUR][1000 genomes]
rs11684995	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11685119	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11689666	0.87[EUR][1000 genomes]
rs11692448	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11695166	0.87[EUR][1000 genomes]
rs11883568	0.87[EUR][1000 genomes]
rs11888626	0.87[EUR][1000 genomes]
rs11894667	0.81[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11894766	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs13010589	0.87[EUR][1000 genomes]
rs13011138	0.87[EUR][1000 genomes]
rs13405019	0.86[EUR][1000 genomes]
rs13415995	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs13416673	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1366672	0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs1583878	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16832396	0.81[LWK][hapmap]
rs16832420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16832456	0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs16832512	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs176712	0.84[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1866849	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1866850	0.83[EUR][1000 genomes]
rs188339	0.81[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs1972288	0.89[EUR][1000 genomes]
rs2067402	0.84[MEX][hapmap];0.92[TSI][hapmap]
rs2067411	0.95[CEU][hapmap]
rs2067418	0.84[CEU][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap]
rs2067419	0.84[CEU][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap]
rs2099127	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2099128	0.87[EUR][1000 genomes]
rs2099129	0.87[EUR][1000 genomes]
rs2136567	0.81[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2136568	0.81[CEU][hapmap]
rs2136571	0.81[CEU][hapmap]
rs2244075	0.87[EUR][1000 genomes]
rs2244076	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2256301	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2271270	0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2303827	0.87[EUR][1000 genomes]
rs2353890	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs2562796	0.81[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs2582738	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2582739	0.81[EUR][1000 genomes]
rs2582740	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2582742	0.81[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2582743	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2582744	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2582745	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2582747	0.80[AMR][1000 genomes]
rs2582753	0.84[MEX][hapmap];0.92[TSI][hapmap]
rs2582757	0.86[EUR][1000 genomes]
rs2582762	0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs2582763	0.87[EUR][1000 genomes]
rs2582769	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2582771	0.85[EUR][1000 genomes]
rs2582772	0.83[EUR][1000 genomes]
rs2582773	0.83[EUR][1000 genomes]
rs2664241	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2664242	0.85[EUR][1000 genomes]
rs2664243	0.82[EUR][1000 genomes]
rs2664244	0.83[EUR][1000 genomes]
rs2664246	0.82[EUR][1000 genomes]
rs2664247	0.83[EUR][1000 genomes]
rs2664249	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2664255	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2664256	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2664261	0.80[AMR][1000 genomes]
rs2664264	0.86[EUR][1000 genomes]
rs2664266	0.82[EUR][1000 genomes]
rs2664267	0.82[EUR][1000 genomes]
rs2664269	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2664272	0.87[EUR][1000 genomes]
rs2664273	0.86[EUR][1000 genomes]
rs2664274	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs2664275	0.87[EUR][1000 genomes]
rs2664276	0.85[EUR][1000 genomes]
rs2664277	0.87[EUR][1000 genomes]
rs28887221	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs291402	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs291403	0.87[EUR][1000 genomes]
rs291404	0.87[EUR][1000 genomes]
rs291405	0.87[EUR][1000 genomes]
rs291407	0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs291409	0.87[EUR][1000 genomes]
rs291410	0.87[EUR][1000 genomes]
rs291411	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs291412	0.87[EUR][1000 genomes]
rs291413	0.87[EUR][1000 genomes]
rs291414	0.87[EUR][1000 genomes]
rs291415	0.87[EUR][1000 genomes]
rs291418	0.81[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs291419	0.86[EUR][1000 genomes]
rs291420	0.86[EUR][1000 genomes]
rs291421	0.83[EUR][1000 genomes]
rs291422	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs291423	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs291424	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs291425	0.86[EUR][1000 genomes]
rs291426	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs291434	0.81[CEU][hapmap]
rs291435	0.81[CEU][hapmap]
rs291436	0.81[CEU][hapmap]
rs291441	0.80[CEU][hapmap]
rs291442	0.81[CEU][hapmap]
rs291450	0.81[EUR][1000 genomes]
rs291451	0.81[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs291455	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2919676	0.81[EUR][1000 genomes]
rs2941092	0.82[EUR][1000 genomes]
rs2966470	0.82[EUR][1000 genomes]
rs34760043	0.89[EUR][1000 genomes]
rs35214387	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3749015	0.87[EUR][1000 genomes]
rs3749016	0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs3762548	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3791788	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3791789	0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs3791790	0.88[EUR][1000 genomes]
rs3791791	0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs3791792	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3791800	1.00[CEU][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3791805	1.00[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3791806	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs3791815	0.84[MEX][hapmap];0.92[TSI][hapmap]
rs3815961	0.89[EUR][1000 genomes]
rs3828269	0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs4853503	0.87[EUR][1000 genomes]
rs4853685	0.81[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs4853687	0.81[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs4853688	0.87[EUR][1000 genomes]
rs4853689	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4853693	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55684836	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55742982	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55815425	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56742312	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56853355	0.89[EUR][1000 genomes]
rs57110838	0.84[EUR][1000 genomes]
rs60068799	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60469543	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61038868	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6434381	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6434382	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6434383	0.81[EUR][1000 genomes]
rs66738092	0.89[EUR][1000 genomes]
rs66867328	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6720060	0.87[EUR][1000 genomes]
rs6723792	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6737514	0.87[EUR][1000 genomes]
rs6737846	0.90[EUR][1000 genomes]
rs6749512	0.87[EUR][1000 genomes]
rs6751238	0.89[EUR][1000 genomes]
rs6751588	0.89[EUR][1000 genomes]
rs6752703	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6753459	0.81[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs713425	0.81[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs713426	0.87[EUR][1000 genomes]
rs72625301	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72625302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72627903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72627904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72627905	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7371399	0.84[EUR][1000 genomes]
rs7371409	0.84[EUR][1000 genomes]
rs7562807	0.81[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7565423	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs7566380	0.87[EUR][1000 genomes]
rs7569296	0.89[EUR][1000 genomes]
rs7573689	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs7574028	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs7574495	0.89[EUR][1000 genomes]
rs7580863	0.87[EUR][1000 genomes]
rs7582209	0.87[EUR][1000 genomes]
rs7583250	0.89[EUR][1000 genomes]
rs7590942	0.89[EUR][1000 genomes]
rs7599085	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7602400	0.87[EUR][1000 genomes]
rs760307	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap]

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	esv3439178	chr2:190877215-191124499	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv875619	chr2:191062951-191112241	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4853684	HIBCH	cis	cerebellum	SCAN
rs4853684	INPP1	cis	cerebellum	SCAN
rs4853684	INPP1	Cis_1M	lymphoblastoid	RTeQTL
rs4853684	HIBCH	cis	parietal	SCAN
rs4853684	HIBCH	Cis_1M	lymphoblastoid	RTeQTL
rs4853684	INPP1	cis	parietal	SCAN
rs4853684	WDR75	cis	lymphoblastoid	seeQTL
rs4853684	INPP1	cis	lymphoblastoid	seeQTL
rs4853684	MFSD6	cis	cerebellum	SCAN
rs4853684	HIBCH	cis	Thyroid	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191046000-191074000	Weak transcription	HMEC	breast
2	chr2:191046000-191088400	Weak transcription	HSMMtube	muscle
3	chr2:191046200-191064200	Weak transcription	HSMM	muscle
4	chr2:191046400-191063600	Weak transcription	HepG2	liver
5	chr2:191046400-191064400	Weak transcription	Pancreas	Pancrea
6	chr2:191046400-191064400	Weak transcription	Psoas Muscle	Psoas
7	chr2:191046400-191070400	Weak transcription	Fetal Stomach	stomach
8	chr2:191046600-191064400	Weak transcription	Brain Angular Gyrus	brain
9	chr2:191046600-191086400	Weak transcription	Colonic Mucosa	Colon
10	chr2:191047000-191080400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:191047600-191081000	Weak transcription	Brain Anterior Caudate	brain
12	chr2:191048200-191073800	Weak transcription	Aorta	Aorta
13	chr2:191049200-191064400	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:191052000-191108800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:191052600-191063000	Weak transcription	Left Ventricle	heart
16	chr2:191053000-191078200	Weak transcription	Right Ventricle	heart
17	chr2:191056600-191070200	Weak transcription	NHDF-Ad	bronchial
18	chr2:191056800-191064400	Weak transcription	Esophagus	oesophagus
19	chr2:191056800-191124600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:191056800-191131800	Weak transcription	NHEK	skin
21	chr2:191057000-191078400	Weak transcription	Thymus	Thymus
22	chr2:191057200-191076200	Weak transcription	Fetal Kidney	kidney
23	chr2:191057800-191087800	Weak transcription	Fetal Brain Female	brain
24	chr2:191058000-191076000	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:191059600-191063800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:191059800-191064400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:191059800-191064600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:191060000-191107000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:191060200-191063600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:191060200-191066600	Weak transcription	Dnd41	blood
31	chr2:191060200-191078600	Weak transcription	NH-A	brain
32	chr2:191060200-191090600	Weak transcription	A549	lung
33	chr2:191060400-191068000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:191060400-191076600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:191060600-191063800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:191060600-191072000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:191060600-191074000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:191060600-191078200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:191060600-191084000	Weak transcription	HUVEC	blood vessel
40	chr2:191060600-191087800	Weak transcription	Brain Germinal Matrix	brain
41	chr2:191060800-191063800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:191060800-191079600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:191060800-191180000	Weak transcription	Small Intestine	intestine
44	chr2:191061000-191064400	Weak transcription	Brain Substantia Nigra	brain
45	chr2:191061000-191070200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:191061000-191089200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr2:191061200-191070200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:191061400-191064600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:191061400-191068600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:191061600-191065000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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