Variant report

Variant	rs3828513
Chromosome Location	chr4:144310659-144310660
allele	A/G
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	TCF12	chr4:144310606-144311157	A549	lung:	n/a	n/a
2	HDAC2	chr4:144310629-144311114	MCF-7	breast:	n/a	chr4:144310681-144310690
3	GATA3	chr4:144310627-144311153	T-47D	breast:	n/a	chr4:144310680-144310690 chr4:144310680-144310689 chr4:144310675-144310696 chr4:144310682-144310689
4	NFIC	chr4:144310603-144311164	HepG2	liver:	n/a	n/a
5	FOSL2	chr4:144310657-144311122	A549	lung:	n/a	chr4:144311080-144311094
6	FOXA1	chr4:144310539-144311139	HepG2	liver:	n/a	n/a
7	MYBL2	chr4:144310595-144311098	HepG2	liver:	n/a	n/a
8	FOXA2	chr4:144310526-144311551	HepG2	liver:	n/a	chr4:144311189-144311201
9	FOXA1	chr4:144310622-144311169	HepG2	liver:	n/a	n/a
10	FOXA2	chr4:144310649-144311141	HepG2	liver:	n/a	n/a
11	FOXA1	chr4:144310623-144311123	HepG2	liver:	n/a	n/a
12	JUND	chr4:144310646-144311160	T-47D	breast:	n/a	chr4:144311080-144311094
13	EP300	chr4:144310589-144311142	T-47D	breast:	n/a	n/a
14	FOXA1	chr4:144310606-144311114	T-47D	breast:	n/a	n/a
15	MBD4	chr4:144310659-144311100	HepG2	liver:	n/a	n/a
16	NR2F2	chr4:144310459-144311061	MCF-7	breast:	n/a	n/a
17	TCF7L2	chr4:144310483-144311046	HepG2	liver:	n/a	chr4:144310959-144310973
18	EP300	chr4:144310579-144311036	HepG2	liver:	n/a	n/a
19	GATA3	chr4:144310577-144311171	MCF-7	breast:	n/a	chr4:144310680-144310690 chr4:144310680-144310689 chr4:144310675-144310696 chr4:144310682-144310689
20	GATA3	chr4:144310514-144311243	SK-N-SH	brain:	n/a	chr4:144310680-144310690 chr4:144310680-144310689 chr4:144310675-144310696 chr4:144310682-144310689
21	TEAD4	chr4:144310510-144311203	HepG2	liver:	n/a	n/a
22	JUND	chr4:144310653-144311212	T-47D	breast:	n/a	chr4:144311080-144311094
23	GATA3	chr4:144310538-144311203	T-47D	breast:	n/a	chr4:144310680-144310690 chr4:144310680-144310689 chr4:144310675-144310696 chr4:144310682-144310689
24	GATA3	chr4:144310480-144311161	MCF-7	breast:	n/a	chr4:144310680-144310690 chr4:144310680-144310689 chr4:144310675-144310696 chr4:144310682-144310689
25	EP300	chr4:144310656-144311113	HepG2	liver:	n/a	n/a
26	TCF7L2	chr4:144310640-144310977	MCF-7	breast:	n/a	chr4:144310959-144310973

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:144308580..144312274-chr4:144317112..144320354,4	K562	blood:

Variant related genes	Relation type
GAB1	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10013047	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1027851	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1027852	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10519691	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap]
rs11100786	0.97[ASN][1000 genomes]
rs11100787	0.96[ASN][1000 genomes]
rs11100788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11100789	0.84[ASN][1000 genomes]
rs11730569	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945731	0.90[ASN][1000 genomes]
rs12647531	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649592	0.97[ASN][1000 genomes]
rs13101346	0.95[ASN][1000 genomes]
rs13123498	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1397526	0.86[ASN][1000 genomes]
rs1397528	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1472873	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510879	0.90[ASN][1000 genomes]
rs1510880	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1866756	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2048408	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119270	0.97[ASN][1000 genomes]
rs2196908	0.95[ASN][1000 genomes]
rs2196909	0.95[ASN][1000 genomes]
rs300890	0.84[JPT][hapmap]
rs300893	0.84[JPT][hapmap]
rs300894	0.84[JPT][hapmap]
rs300895	0.84[JPT][hapmap]
rs300904	0.84[JPT][hapmap]
rs300905	0.84[JPT][hapmap]
rs300910	0.86[ASN][1000 genomes]
rs300911	0.89[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs300912	0.89[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs300913	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs300914	0.82[CEU][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs300915	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs300916	0.89[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs300917	0.82[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs300918	0.82[ASN][1000 genomes]
rs300919	0.84[JPT][hapmap]
rs34095331	0.88[ASN][1000 genomes]
rs34439737	0.93[ASN][1000 genomes]
rs3792652	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792653	0.97[ASN][1000 genomes]
rs3792655	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805238	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.88[ASN][1000 genomes]
rs3805245	0.97[ASN][1000 genomes]
rs3805246	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805247	0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805251	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3805252	0.97[ASN][1000 genomes]
rs3805253	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3805254	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805256	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3805257	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3828514	0.97[ASN][1000 genomes]
rs55758499	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55894236	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537154	0.96[ASN][1000 genomes]
rs6537155	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs713140	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs719392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7680959	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs906571	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3828513	ABCE1	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144302800-144312600	Weak transcription	Placenta	Placenta
2	chr4:144303000-144312000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:144303000-144318000	Weak transcription	HSMM	muscle
4	chr4:144303200-144311800	Weak transcription	Brain Germinal Matrix	brain
5	chr4:144303200-144312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:144303200-144317800	Weak transcription	Gastric	stomach
7	chr4:144303400-144312000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:144303400-144312600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:144303400-144326600	Weak transcription	Colonic Mucosa	Colon
10	chr4:144304200-144320000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:144304400-144312000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:144304600-144311200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:144304600-144312600	Weak transcription	HSMMtube	muscle
14	chr4:144304600-144317000	Weak transcription	K562	blood
15	chr4:144305200-144311000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr4:144305200-144311800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:144305200-144311800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:144306000-144312000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:144306000-144312000	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:144306000-144312000	Weak transcription	Pancreas	Pancrea
21	chr4:144306200-144311000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:144306200-144311200	Enhancers	Brain Angular Gyrus	brain
23	chr4:144306600-144312000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:144306600-144318000	Weak transcription	Aorta	Aorta
25	chr4:144307000-144311800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:144307400-144312000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:144307400-144323600	Enhancers	Brain Hippocampus Middle	brain
28	chr4:144307800-144311800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:144307800-144313000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr4:144308000-144313400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr4:144308000-144316400	Enhancers	Brain Substantia Nigra	brain
32	chr4:144308200-144311000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:144308200-144311400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:144308200-144311600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr4:144308200-144313800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:144308600-144313000	Enhancers	Primary B cells from cord blood	blood
37	chr4:144308600-144315400	Enhancers	Fetal Lung	lung
38	chr4:144308800-144311000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:144308800-144311400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr4:144308800-144311800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr4:144308800-144312400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr4:144308800-144313000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr4:144308800-144319400	Enhancers	Brain Cingulate Gyrus	brain
44	chr4:144309200-144311600	Weak transcription	Fetal Intestine Large	intestine
45	chr4:144309200-144312000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:144309200-144312000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:144309200-144312000	Weak transcription	Fetal Brain Female	brain
48	chr4:144309200-144312000	Weak transcription	Ovary	ovary
49	chr4:144309200-144312000	Weak transcription	Right Ventricle	heart
50	chr4:144309200-144317000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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