Variant report

Variant	rs2385867
Chromosome Location	chr3:47059323-47059324
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	chr3:46985961..46989571-chr3:47058662..47060411,3	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10433549	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs10461018	0.92[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1079276	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1108301	0.93[EUR][1000 genomes]
rs11130110	0.92[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130111	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130112	0.92[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11130114	0.81[ASN][1000 genomes]
rs11130115	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs11707736	0.83[EUR][1000 genomes]
rs11709660	0.85[EUR][1000 genomes]
rs11715121	0.85[EUR][1000 genomes]
rs11716553	0.87[EUR][1000 genomes]
rs11719795	0.81[JPT][hapmap]
rs11720139	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs11917361	0.86[EUR][1000 genomes]
rs11917474	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12152493	0.92[EUR][1000 genomes]
rs12491473	0.89[EUR][1000 genomes]
rs12630534	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12715421	0.85[EUR][1000 genomes]
rs13061071	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13062681	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13066214	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077398	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13087426	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13091054	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13094672	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13098228	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1463393	0.89[EUR][1000 genomes]
rs1466741	0.84[CEU][hapmap]
rs17784127	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1869869	0.93[EUR][1000 genomes]
rs1869871	0.84[EUR][1000 genomes]
rs2061197	0.92[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2132173	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs2278963	0.89[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2290546	0.81[JPT][hapmap]
rs2305634	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305635	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs2305638	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34103310	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34344887	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4078466	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4082155	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4234465	0.92[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs4587	0.81[JPT][hapmap]
rs4682831	0.93[EUR][1000 genomes]
rs4682837	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682844	0.92[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs4682852	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4683297	0.81[JPT][hapmap]
rs4683298	0.81[JPT][hapmap]
rs4683320	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683322	0.89[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs55724164	0.89[EUR][1000 genomes]
rs55843455	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55927279	0.87[EUR][1000 genomes]
rs56217494	0.86[EUR][1000 genomes]
rs56249396	0.87[EUR][1000 genomes]
rs61729713	0.93[EUR][1000 genomes]
rs62246375	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62246398	0.88[EUR][1000 genomes]
rs62248439	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6414435	0.83[EUR][1000 genomes]
rs6442040	0.81[JPT][hapmap]
rs6442055	0.84[EUR][1000 genomes]
rs66539935	0.93[EUR][1000 genomes]
rs66564457	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6763236	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6767218	0.88[EUR][1000 genomes]
rs6767907	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs6768722	0.85[EUR][1000 genomes]
rs6772670	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6774733	0.90[EUR][1000 genomes]
rs6777145	0.84[EUR][1000 genomes]
rs6785790	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794193	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6808742	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7433300	0.85[CEU][hapmap]
rs749511	0.89[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs749512	0.82[CEU][hapmap]
rs7610620	0.82[EUR][1000 genomes]
rs7610636	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617689	0.89[EUR][1000 genomes]
rs7621911	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7625067	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7625070	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7628747	0.92[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7633698	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636252	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637302	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7640397	0.90[EUR][1000 genomes]
rs7645278	0.81[JPT][hapmap]
rs9311403	0.92[CEU][hapmap]
rs9837343	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs9844122	0.84[EUR][1000 genomes]
rs9845728	0.84[EUR][1000 genomes]
rs9852082	0.81[JPT][hapmap]
rs9854790	0.84[EUR][1000 genomes]
rs9855938	0.81[JPT][hapmap]
rs9858443	0.85[EUR][1000 genomes]
rs9875235	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2385867	PRKAR2A	cis	cerebellum	SCAN
rs2385867	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs2385867	C3orf75	cis	cerebellum	SCAN
rs2385867	RTP3	cis	lesional skin	skin_eQTL
rs2385867	CCDC12	cis	cerebellum	SCAN
rs2385867	SCAP	cis	parietal	SCAN
rs2385867	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs2385867	HYAL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47050200-47063800	Weak transcription	Stomach Mucosa	stomach
2	chr3:47051400-47064000	Weak transcription	Small Intestine	intestine
3	chr3:47051800-47060400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:47051800-47061600	Weak transcription	Right Atrium	heart
5	chr3:47051800-47062000	Weak transcription	Psoas Muscle	Psoas
6	chr3:47052000-47062200	Strong transcription	Fetal Stomach	stomach
7	chr3:47052400-47061200	Strong transcription	Spleen	Spleen
8	chr3:47053200-47062400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr3:47053400-47062200	Strong transcription	Fetal Muscle Leg	muscle
10	chr3:47054000-47061800	Strong transcription	Placenta	Placenta
11	chr3:47054200-47061600	Genic enhancers	Fetal Intestine Small	intestine
12	chr3:47054200-47062400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:47054400-47059800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:47054400-47061400	Strong transcription	Stomach Smooth Muscle	stomach
15	chr3:47054400-47062000	Strong transcription	Adipose Nuclei	Adipose
16	chr3:47054600-47062800	Strong transcription	Fetal Brain Female	brain
17	chr3:47054800-47059600	Strong transcription	Esophagus	oesophagus
18	chr3:47054800-47060600	Weak transcription	Fetal Heart	heart
19	chr3:47054800-47060800	Weak transcription	Fetal Brain Male	brain
20	chr3:47055000-47059800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:47055000-47061600	Strong transcription	Brain Hippocampus Middle	brain
22	chr3:47055000-47062000	Strong transcription	Brain Cingulate Gyrus	brain
23	chr3:47055000-47062400	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:47055200-47061400	Genic enhancers	Fetal Thymus	thymus
25	chr3:47055400-47061800	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr3:47055400-47062200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:47055400-47063000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:47055600-47061600	Strong transcription	Left Ventricle	heart
29	chr3:47055600-47061800	Strong transcription	Brain Angular Gyrus	brain
30	chr3:47055600-47062000	Strong transcription	Brain Substantia Nigra	brain
31	chr3:47055600-47062000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr3:47056400-47061800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:47056600-47059600	Genic enhancers	Liver	Liver
34	chr3:47056600-47062200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:47056800-47059600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:47056800-47059800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:47056800-47059800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:47056800-47059800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr3:47056800-47061000	Strong transcription	Rectal Smooth Muscle	rectum
40	chr3:47056800-47061200	Genic enhancers	Fetal Intestine Large	intestine
41	chr3:47056800-47061800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:47056800-47062000	Strong transcription	Fetal Lung	lung
43	chr3:47056800-47062400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:47057000-47059800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:47057000-47061000	Strong transcription	Colon Smooth Muscle	Colon
46	chr3:47057000-47061200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:47057200-47066600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:47057400-47061200	Strong transcription	Right Ventricle	heart
49	chr3:47057600-47059400	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr3:47057600-47059400	Genic enhancers	NHLF	lung

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