Variant report

Variant	rs16846347
Chromosome Location	chr3:98496468-98496469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr3:98496166-98496503	T-47D	breast:	n/a	n/a
2	HDAC2	chr3:98496037-98496615	HepG2	liver:	n/a	n/a
3	CEBPB	chr3:98496062-98496468	HepG2	liver:	n/a	n/a
4	GATA3	chr3:98496232-98496500	T-47D	breast:	n/a	n/a
5	FOXA1	chr3:98496060-98496561	HepG2	liver:	n/a	n/a
6	ZEB1	chr3:98495890-98497201	HepG2	liver:	n/a	chr3:98497020-98497032
7	RXRA	chr3:98496120-98496471	HepG2	liver:	n/a	n/a
8	HNF4G	chr3:98496144-98496506	HepG2	liver:	n/a	n/a
9	ARID3A	chr3:98496096-98496551	HepG2	liver:	n/a	n/a
10	FOXA1	chr3:98496073-98496661	HepG2	liver:	n/a	n/a
11	FOXA1	chr3:98496051-98496617	HepG2	liver:	n/a	n/a
12	ZEB1	chr3:98495953-98496661	HepG2	liver:	n/a	n/a
13	TEAD4	chr3:98495935-98496676	HepG2	liver:	n/a	n/a
14	FOXA1	chr3:98496172-98496599	T-47D	breast:	n/a	n/a
15	USF2	chr3:98496147-98496524	HepG2	liver:	n/a	n/a
16	FOXA2	chr3:98496022-98496596	HepG2	liver:	n/a	n/a
17	GATA3	chr3:98496144-98496554	T-47D	breast:	n/a	n/a
18	EP300	chr3:98496023-98496640	HepG2	liver:	n/a	n/a
19	FOXA1	chr3:98496029-98496627	HepG2	liver:	n/a	n/a
20	SP1	chr3:98496044-98496597	HepG2	liver:	n/a	n/a
21	TEAD4	chr3:98496255-98496486	HepG2	liver:	n/a	n/a
22	HNF4A	chr3:98496094-98496508	HepG2	liver:	n/a	n/a
23	EP300	chr3:98496096-98496567	HepG2	liver:	n/a	n/a
24	FOXA2	chr3:98495728-98496808	HepG2	liver:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98494773..98497684-chr3:98500222..98503484,3	K562	blood:

No data

Variant related genes	Relation type
PDLIM1P4	TF binding region
ENSG00000064225	Chromatin interaction
ENSG00000249274	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10433438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10511169	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10935518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10935542	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap]
rs11716579	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11914715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1440154	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16840260	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17210963	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs17852693	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1822017	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1827158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55650073	0.88[EUR][1000 genomes]
rs55662129	0.92[EUR][1000 genomes]
rs55730510	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55988144	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56075614	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56290036	0.92[EUR][1000 genomes]
rs56322058	0.88[EUR][1000 genomes]
rs6440159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6805605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs73136038	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136045	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73136048	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73136057	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73136060	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73138004	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73138027	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73138030	0.92[EUR][1000 genomes]
rs73138048	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73138053	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73138055	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73138058	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73138063	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73138082	0.88[EUR][1000 genomes]
rs73140009	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7614892	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7629550	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs7644946	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8179927	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16846347	OR5K2	cis	parietal	SCAN
rs16846347	CEP97	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
3	chr3:98482800-98497400	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:98483000-98497400	Weak transcription	Spleen	Spleen
5	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
8	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
13	chr3:98488200-98496800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:98488600-98497200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:98488600-98497200	Weak transcription	Fetal Kidney	kidney
16	chr3:98489600-98497000	Weak transcription	Lung	lung
17	chr3:98489800-98496600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:98489800-98496600	Weak transcription	Adipose Nuclei	Adipose
19	chr3:98489800-98497000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:98489800-98497400	Weak transcription	Right Ventricle	heart
21	chr3:98489800-98497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
23	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:98490400-98497400	Weak transcription	Fetal Brain Female	brain
25	chr3:98491600-98496600	Strong transcription	Primary hematopoietic stem cells	blood
26	chr3:98491600-98497400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:98493600-98496800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:98493800-98498400	Enhancers	HepG2	liver
30	chr3:98493800-98499600	Enhancers	Fetal Intestine Large	intestine
31	chr3:98494000-98497000	Strong transcription	Thymus	Thymus
32	chr3:98494400-98497200	Genic enhancers	Monocytes-CD14+_RO01746	blood
33	chr3:98494400-98498400	Enhancers	Fetal Intestine Small	intestine
34	chr3:98494600-98497600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:98494600-98499200	Genic enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:98494600-98506000	Enhancers	Aorta	Aorta
37	chr3:98494800-98497000	Weak transcription	GM12878-XiMat	blood
38	chr3:98495200-98496800	Strong transcription	Fetal Thymus	thymus
39	chr3:98495200-98497600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:98495200-98498000	Enhancers	Pancreas	Pancrea
41	chr3:98495400-98497200	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr3:98495600-98497200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:98495600-98497200	Enhancers	HMEC	breast
44	chr3:98495800-98496600	Strong transcription	Dnd41	blood
45	chr3:98495800-98497400	Enhancers	Osteobl	bone
46	chr3:98495800-98497800	Enhancers	HUVEC	blood vessel
47	chr3:98495800-98498000	Enhancers	Gastric	stomach
48	chr3:98495800-98499200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr3:98495800-98499600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr3:98496000-98497200	Enhancers	Brain Angular Gyrus	brain

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