Variant report

Variant	rs1800804
Chromosome Location	chr4:100495817-100495818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:100495806-100496304	HepG2	liver:	n/a	n/a
2	SP1	chr4:100495638-100496247	HepG2	liver:	n/a	n/a
3	FOXA1	chr4:100495665-100496171	HepG2	liver:	n/a	n/a
4	FOXA2	chr4:100495728-100496173	HepG2	liver:	n/a	n/a
5	FOXA1	chr4:100495662-100496202	HepG2	liver:	n/a	n/a
6	HNF4A	chr4:100495699-100496153	HepG2	liver:	n/a	chr4:100495926-100495948 chr4:100495931-100495943 chr4:100495898-100495911 chr4:100495898-100495911
7	NFIC	chr4:100495688-100496214	HepG2	liver:	n/a	n/a
8	HDAC2	chr4:100495709-100496105	HepG2	liver:	n/a	n/a
9	FOXA2	chr4:100495563-100496461	HepG2	liver:	n/a	n/a
10	HNF4G	chr4:100495675-100496262	HepG2	liver:	n/a	chr4:100495926-100495948 chr4:100495931-100495943 chr4:100495898-100495911 chr4:100495898-100495911
11	HNF4A	chr4:100495731-100496217	HepG2	liver:	n/a	chr4:100495926-100495948 chr4:100495931-100495943 chr4:100495898-100495911 chr4:100495898-100495911
12	YY1	chr4:100495761-100496161	H1-hESC	embryonic stem cell:	n/a	n/a
13	TBP	chr4:100495794-100496172	HepG2	liver:	n/a	n/a
14	MBD4	chr4:100495703-100496349	HepG2	liver:	n/a	n/a
15	HNF4A	chr4:100495749-100496133	HepG2	liver:	n/a	chr4:100495926-100495948 chr4:100495931-100495943 chr4:100495898-100495911 chr4:100495898-100495911
16	MAZ	chr4:100495785-100496130	HepG2	liver:	n/a	n/a
17	RXRA	chr4:100495738-100496111	HepG2	liver:	n/a	chr4:100495931-100495945
18	HDAC2	chr4:100495705-100496198	HepG2	liver:	n/a	n/a
19	EP300	chr4:100495815-100496501	GM12878	blood:	n/a	n/a
20	ARID3A	chr4:100495701-100496496	HepG2	liver:	n/a	n/a
21	REST	chr4:100495763-100496250	HepG2	liver:	n/a	n/a
22	MYBL2	chr4:100495474-100496594	HepG2	liver:	n/a	n/a
23	E2F4	chr4:100495774-100495957	MCF10A-Er-Src	breast:	n/a	n/a
24	FOXA1	chr4:100495796-100496206	HepG2	liver:	n/a	n/a
25	EP300	chr4:100495667-100496229	HepG2	liver:	n/a	n/a
26	NR2F2	chr4:100495592-100496362	HepG2	liver:	n/a	n/a
27	HEY1	chr4:100495684-100496359	HepG2	liver:	n/a	n/a
28	ZBTB7A	chr4:100495768-100496180	HepG2	liver:	n/a	n/a
29	NFIC	chr4:100495659-100496373	HepG2	liver:	n/a	n/a
30	SIN3AK20	chr4:100495787-100496211	HepG2	liver:	n/a	n/a
31	NR2F2	chr4:100495716-100496297	HepG2	liver:	n/a	n/a
32	MYBL2	chr4:100495687-100496289	HepG2	liver:	n/a	n/a
33	HNF4G	chr4:100495746-100496149	HepG2	liver:	n/a	chr4:100495926-100495948 chr4:100495931-100495943 chr4:100495898-100495911 chr4:100495898-100495911
34	ZNF384	chr4:100495620-100496670	GM12878	blood:	n/a	n/a
35	TEAD4	chr4:100495534-100496467	HepG2	liver:	n/a	n/a
36	FOXA1	chr4:100495676-100496242	HepG2	liver:	n/a	n/a
37	EP300	chr4:100495693-100496094	HepG2	liver:	n/a	n/a
38	YY1	chr4:100495762-100496222	HepG2	liver:	n/a	chr4:100496158-100496174
39	POLR2A	chr4:100495759-100496300	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:100483825..100487294-chr4:100492777..100496037,4	K562	blood:
2	chr4:100483825..100487771-chr4:100493784..100496037,3	K562	blood:

Variant related genes	Relation type
MTTP	TF binding region
ENSG00000138823	Chromatin interaction
ENSG00000145331	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10000018	0.86[EUR][1000 genomes]
rs10007794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10008896	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10008928	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10009198	0.84[EUR][1000 genomes]
rs10013868	0.91[ASN][1000 genomes]
rs10013883	0.87[ASN][1000 genomes]
rs10019266	0.86[EUR][1000 genomes]
rs10020461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10022775	0.91[ASN][1000 genomes]
rs10026790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10031512	0.86[EUR][1000 genomes]
rs10516443	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10516444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1054730	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1057615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097668	0.97[ASN][1000 genomes]
rs11933250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933337	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11933520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933937	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934921	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11935423	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];0.97[ASN][1000 genomes]
rs11935581	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11937107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11937273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11943031	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944749	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11944750	0.91[ASN][1000 genomes]
rs11944752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946292	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11946367	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11946658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11947558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491235	0.95[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs1503774	0.85[EUR][1000 genomes]
rs1503777	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1503778	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17029108	0.86[EUR][1000 genomes]
rs17029163	1.00[ASN][1000 genomes]
rs17531824	0.93[ASN][1000 genomes]
rs17598226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873517	0.84[EUR][1000 genomes]
rs2089079	0.95[CEU][hapmap];0.95[GIH][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs2255119	0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2637768	0.95[ASN][1000 genomes]
rs2718684	0.95[ASN][1000 genomes]
rs28368786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28431971	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28435607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28444681	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28473262	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28497720	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28500697	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851225	0.95[ASN][1000 genomes]
rs28595160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608631	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28621060	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28647519	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866164	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28666735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28678377	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28704064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28789770	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28849180	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903201	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3811800	0.81[CEU][hapmap]
rs3816873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[ASN][1000 genomes]
rs4423880	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45440196	0.88[ASN][1000 genomes]
rs6532820	0.86[EUR][1000 genomes]
rs6815231	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6815416	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6825248	0.95[ASN][1000 genomes]
rs6839296	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841211	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6841282	0.91[ASN][1000 genomes]
rs6854911	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs72681967	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7656665	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661453	0.86[EUR][1000 genomes]
rs7661656	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7661964	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682548	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686425	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7687762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693203	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693979	0.82[EUR][1000 genomes]
rs867380	0.85[EUR][1000 genomes]
rs867381	0.85[EUR][1000 genomes]
rs884274	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs884275	0.81[CEU][hapmap]
rs9307240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990558	0.84[EUR][1000 genomes]
rs9997840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
2	nsv933074	chr4:100460951-100630600	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1833664	chr4:100495571-100504985	Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1800804	TRIM60	trans	parietal	SCAN
rs1800804	ADH6	cis	parietal	SCAN
rs1800804	C4orf37	cis	cerebellum	SCAN
rs1800804	MTTP	cis	lymphoblastoid	seeQTL
rs1800804	TSPAN5	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100495000-100496400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:100495200-100496000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:100495200-100496000	Flanking Active TSS	HepG2	liver
4	chr4:100495400-100496200	Flanking Active TSS	Liver	Liver
5	chr4:100495400-100497000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:100495600-100496000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:100495600-100496000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr4:100495600-100497000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr4:100495600-100497200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:100495600-100500400	Active TSS	Fetal Intestine Large	intestine
11	chr4:100495800-100496000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr4:100495800-100496000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr4:100495800-100496200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:100495800-100496200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr4:100495800-100496200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:100495800-100496200	Enhancers	Colon Smooth Muscle	Colon
17	chr4:100495800-100496200	Active TSS	Rectal Smooth Muscle	rectum
18	chr4:100495800-100496200	Enhancers	Stomach Mucosa	stomach
19	chr4:100495800-100496400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr4:100495800-100496400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr4:100495800-100496400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr4:100495800-100496400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr4:100495800-100496400	Enhancers	Primary B cells from cord blood	blood
24	chr4:100495800-100496400	Active TSS	Brain Anterior Caudate	brain
25	chr4:100495800-100496400	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr4:100495800-100496600	Enhancers	Primary B cells from peripheral blood	blood
27	chr4:100495800-100496600	Active TSS	Aorta	Aorta
28	chr4:100495800-100496600	Active TSS	Ovary	ovary
29	chr4:100495800-100496600	Flanking Active TSS	GM12878-XiMat	blood
30	chr4:100495800-100500400	Active TSS	Fetal Intestine Small	intestine
31	chr4:100495800-100500800	Active TSS	Duodenum Mucosa	Duodenum

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