Variant report

Variant	rs1799843
Chromosome Location	chr3:49849723-49849724
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49823748..49825794-chr3:49847684..49850638,2	MCF-7	breast:
2	chr3:49842643..49844250-chr3:49847224..49849823,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182179	Chromatin interaction
ENSG00000176095	Chromatin interaction
ENSG00000263506	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10049413	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1049256	0.90[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10865958	0.96[ASN][1000 genomes]
rs10865959	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130214	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130216	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130218	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11130219	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11130221	0.89[ASN][1000 genomes]
rs1128535	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11709573	0.89[CHB][hapmap]
rs11709680	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11710675	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714957	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11715304	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11716575	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11717256	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717463	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11920900	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12381242	0.87[ASN][1000 genomes]
rs12490656	0.84[ASN][1000 genomes]
rs12496226	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12634780	0.86[CHB][hapmap]
rs13063621	0.89[ASN][1000 genomes]
rs13084243	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13085679	0.96[ASN][1000 genomes]
rs13086130	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13086465	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13090611	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1317140	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13316065	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491986	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs17657664	0.89[CHB][hapmap]
rs17657688	0.89[CHB][hapmap]
rs1799845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234391	0.81[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2246832	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2247036	0.94[ASN][1000 genomes]
rs2271960	0.81[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2271961	0.81[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2276864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291542	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2307021	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2352967	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2352969	0.89[CHB][hapmap]
rs2352974	0.81[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2352975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2352984	0.89[CHB][hapmap]
rs2624819	0.89[CHB][hapmap]
rs2624821	0.89[CHB][hapmap]
rs2681779	0.89[CHB][hapmap]
rs34451146	0.89[ASN][1000 genomes]
rs34522271	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34614773	0.87[ASN][1000 genomes]
rs34735338	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35210174	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35261599	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs35474403	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749237	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749240	0.90[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs3749241	0.89[ASN][1000 genomes]
rs3774759	0.89[CHB][hapmap]
rs3811695	0.85[ASN][1000 genomes]
rs3811696	0.87[ASN][1000 genomes]
rs3819325	0.90[ASN][1000 genomes]
rs4519692	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4688688	0.89[CHB][hapmap]
rs4768	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4855841	0.84[ASN][1000 genomes]
rs4855850	0.87[ASN][1000 genomes]
rs4855862	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855867	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs57648519	0.89[ASN][1000 genomes]
rs59906301	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60205400	0.89[ASN][1000 genomes]
rs62260715	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260719	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260729	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6446295	0.92[ASN][1000 genomes]
rs6766836	0.89[ASN][1000 genomes]
rs6774354	0.89[CHB][hapmap]
rs6775384	0.81[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6785549	0.96[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs6802890	0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs6804655	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs695238	0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs71324996	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7372725	0.83[ASN][1000 genomes]
rs7372730	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs7372966	0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs7374183	0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs7374277	0.83[ASN][1000 genomes]
rs7429353	0.83[ASN][1000 genomes]
rs7431078	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7431106	0.95[CHD][hapmap];0.86[GIH][hapmap];0.89[ASN][1000 genomes]
rs7615206	0.89[CHB][hapmap]
rs7618501	0.91[ASN][1000 genomes]
rs7618519	0.92[ASN][1000 genomes]
rs7627864	0.89[CHB][hapmap]
rs7629936	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7634886	0.87[ASN][1000 genomes]
rs7634902	0.90[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7645061	0.81[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7648987	0.81[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7649348	0.90[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs868891	0.89[CHB][hapmap]
rs9814765	0.87[ASN][1000 genomes]
rs9815766	0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs9819511	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9850465	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9853458	0.87[ASN][1000 genomes]
rs9855505	0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs9859153	0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs9865480	0.87[ASN][1000 genomes]
rs9871654	0.88[ASN][1000 genomes]
rs9872864	0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs9873183	0.83[ASN][1000 genomes]
rs9876508	0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9882639	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv967270	chr3:49845381-49870409	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1799843	WDR6	cis	Whole Blood	GTEx
rs1799843	C3orf54	cis	cerebellum	SCAN
rs1799843	CSPG5	cis	cerebellum	SCAN
rs1799843	RNF123	cis	cerebellum	SCAN
rs1799843	ALS2CL	cis	cerebellum	SCAN
rs1799843	RBM6	cis	parietal	SCAN
rs1799843	P4HTM	cis	parietal	SCAN
rs1799843	WDR6	cis	parietal	SCAN
rs1799843	UCN2	cis	cerebellum	SCAN
rs1799843	CCDC71	cis	cerebellum	SCAN
rs1799843	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs1799843	QRICH1	cis	parietal	SCAN
rs1799843	RBM6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49841600-49850400	Weak transcription	Small Intestine	intestine
2	chr3:49842000-49850600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:49843400-49866400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:49843600-49850400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:49843600-49850600	Weak transcription	HSMM	muscle
6	chr3:49843600-49850800	Weak transcription	Psoas Muscle	Psoas
7	chr3:49844000-49850200	Weak transcription	NHDF-Ad	bronchial
8	chr3:49844400-49850200	Genic enhancers	Spleen	Spleen
9	chr3:49845000-49850600	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr3:49845000-49850600	Weak transcription	NH-A	brain
11	chr3:49845200-49850000	Strong transcription	Colonic Mucosa	Colon
12	chr3:49845400-49849800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:49845400-49850000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:49845400-49850000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:49845400-49850000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:49845400-49850000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:49845400-49850000	Weak transcription	Stomach Mucosa	stomach
18	chr3:49845400-49850600	Weak transcription	HepG2	liver
19	chr3:49845600-49850000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:49845600-49850000	Weak transcription	HMEC	breast
21	chr3:49845600-49850600	Weak transcription	HUVEC	blood vessel
22	chr3:49845600-49850800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:49845800-49849800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:49845800-49849800	Weak transcription	Right Atrium	heart
25	chr3:49845800-49850400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:49845800-49850400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:49845800-49850800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:49846000-49849800	Strong transcription	Fetal Intestine Small	intestine
29	chr3:49846000-49849800	Strong transcription	Gastric	stomach
30	chr3:49846000-49850600	Weak transcription	NHEK	skin
31	chr3:49846200-49849800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:49846200-49850000	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:49846200-49850200	Strong transcription	Fetal Intestine Large	intestine
34	chr3:49846200-49850200	Strong transcription	Thymus	Thymus
35	chr3:49846200-49850600	Weak transcription	Fetal Heart	heart
36	chr3:49846400-49849800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:49846400-49849800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr3:49846400-49849800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr3:49846400-49850000	Strong transcription	Osteobl	bone
40	chr3:49846400-49850800	Weak transcription	Fetal Kidney	kidney
41	chr3:49846400-49850800	Weak transcription	K562	blood
42	chr3:49846600-49849800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:49846600-49849800	Strong transcription	Right Ventricle	heart
44	chr3:49846600-49849800	Strong transcription	Dnd41	blood
45	chr3:49846600-49850200	Strong transcription	Primary T cells from cord blood	blood
46	chr3:49846600-49850200	Genic enhancers	Primary hematopoietic stem cells	blood
47	chr3:49846800-49849800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:49846800-49850000	Strong transcription	NHLF	lung
49	chr3:49847000-49849800	Strong transcription	Fetal Lung	lung
50	chr3:49847000-49850000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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