Variant report

Variant	rs1034400
Chromosome Location	chr4:2932589-2932590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:2929559-2936017	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:2930254-2934156	A549	lung:	n/a	n/a
3	POLR2A	chr4:2932331-2934648	K562	blood:	n/a	n/a
4	POLR2A	chr4:2932498-2933468	K562	blood:	n/a	n/a
5	POLR2A	chr4:2932509-2932889	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr4:2931841-2932706	K562	blood:	n/a	n/a
7	POLR2A	chr4:2932566-2933774	A549	lung:	n/a	n/a
8	POLR2A	chr4:2930058-2935267	GM12892	blood:	n/a	n/a
9	POLR2A	chr4:2932140-2932739	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:2932449-2934032	GM12891	blood:	n/a	n/a
11	POLR2A	chr4:2929805-2936295	HL-60	blood:	n/a	n/a
12	POLR2A	chr4:2931859-2933573	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chr4:2932523-2932917	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr4:2932520-2932670	NHEK	skin:	n/a	n/a
15	EBF1	chr4:2932497-2932954	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:2930022-2934363	GM12892	blood:	n/a	n/a
17	SRF	chr4:2931936-2932602	MCF-7	breast:	n/a	chr4:2932262-2932280 chr4:2932264-2932282
18	POLR2A	chr4:2932354-2934493	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:2932480-2934004	GM12891	blood:	n/a	n/a
20	FOXA1	chr4:2932506-2932902	T-47D	breast:	n/a	n/a
21	POLR2A	chr4:2932520-2934181	GM12892	blood:	n/a	n/a
22	POLR2A	chr4:2930118-2940539	K562	blood:	n/a	n/a
23	EP300	chr4:2932507-2933002	T-47D	breast:	n/a	n/a
24	POLR2A	chr4:2932494-2933996	GM12878	blood:	n/a	n/a
25	POLR2A	chr4:2932094-2934114	HepG2	liver:	n/a	n/a
26	POLR2A	chr4:2930179-2933129	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr4:2932470-2933003	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr4:2932495-2934626	GM12891	blood:	n/a	n/a
29	FOXA1	chr4:2932529-2932898	T-47D	breast:	n/a	n/a
30	POLR2A	chr4:2932421-2934495	GM12878	blood:	n/a	n/a
31	POLR2A	chr4:2930571-2934637	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr4:2930926-2932605	K562	blood:	n/a	n/a
33	POLR2A	chr4:2930187-2932645	GM12892	blood:	n/a	n/a
34	POLR2A	chr4:2931577-2935568	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr4:2931820-2933264	MCF-7	breast:	n/a	n/a
36	POLR2A	chr4:2930108-2936184	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:2931780-2933006	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr4:2932454-2932999	H1-neurons	neurons:	n/a	n/a
39	PML	chr4:2932466-2932823	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:2930105-2936184	HL-60	blood:	n/a	n/a
41	POLR2A	chr4:2932413-2934316	GM19193	blood:	n/a	n/a
42	CTCF	chr4:2932559-2932972	T-47D	breast:	n/a	n/a
43	POLR2A	chr4:2930406-2935196	K562	blood:	n/a	n/a
44	POLR2A	chr4:2932303-2935919	SK-N-MC	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
2	chr4:2905536..2909706-chr4:2929255..2933631,5	MCF-7	breast:
3	chr4:2818050..2820446-chr4:2931198..2934919,4	MCF-7	breast:
4	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
5	chr4:2753882..2759883-chr4:2932429..2941474,15	MCF-7	breast:
6	chr4:2798213..2801828-chr4:2930948..2933812,4	MCF-7	breast:
7	chr4:2838331..2841092-chr4:2930392..2932648,2	MCF-7	breast:
8	chr4:2900149..2902689-chr4:2931088..2933616,2	MCF-7	breast:
9	chr4:2844667..2846499-chr4:2932403..2934582,2	MCF-7	breast:

No data

Variant related genes	Relation type
NOP14-AS1	TF binding region
ENSG00000087266	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10026792	1.00[CHB][hapmap]
rs10488838	1.00[ASN][1000 genomes]
rs1263331	1.00[ASN][1000 genomes]
rs13106867	1.00[CHD][hapmap]
rs1574473	1.00[ASN][1000 genomes]
rs16843169	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843451	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs16843454	1.00[ASN][1000 genomes]
rs16843481	1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];1.00[ASN][1000 genomes]
rs16843500	1.00[ASN][1000 genomes]
rs16843535	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843539	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843553	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16843596	1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17833172	1.00[CHB][hapmap]
rs17833250	1.00[CHB][hapmap]
rs1877723	1.00[CHB][hapmap]
rs2005451	1.00[ASN][1000 genomes]
rs2857845	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2858039	1.00[CHB][hapmap]
rs3213502	1.00[CHB][hapmap]
rs34120252	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34241425	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34550139	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585460	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743278	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34745961	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34945392	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35445752	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35508581	1.00[ASN][1000 genomes]
rs35893718	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35913891	1.00[ASN][1000 genomes]
rs36038921	1.00[ASN][1000 genomes]
rs3733220	1.00[CHD][hapmap];1.00[LWK][hapmap]
rs41528047	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs4690006	1.00[CHB][hapmap]
rs4741	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4969	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56975682	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57155428	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57174035	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57557041	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57763208	1.00[ASN][1000 genomes]
rs58059873	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58132256	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58196520	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58731679	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58758786	1.00[ASN][1000 genomes]
rs58928665	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59426248	1.00[ASN][1000 genomes]
rs59786983	1.00[ASN][1000 genomes]
rs59790260	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59798370	1.00[ASN][1000 genomes]
rs60169711	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61117606	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61339714	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678161	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2893200-2932600	Strong transcription	Fetal Thymus	thymus
2	chr4:2901200-2934600	Weak transcription	Hela-S3	cervix
3	chr4:2907400-2935400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:2911200-2935000	Weak transcription	Psoas Muscle	Psoas
5	chr4:2912600-2934800	Weak transcription	A549	lung
6	chr4:2913000-2935000	Weak transcription	K562	blood
7	chr4:2915600-2933000	Weak transcription	Right Atrium	heart
8	chr4:2923800-2933600	Strong transcription	Thymus	Thymus
9	chr4:2924000-2934400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:2924200-2932600	Strong transcription	Rectal Smooth Muscle	rectum
11	chr4:2924200-2932600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:2924200-2932800	Strong transcription	Adipose Nuclei	Adipose
13	chr4:2924200-2933000	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr4:2924200-2934400	Strong transcription	Fetal Stomach	stomach
15	chr4:2924200-2934800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:2924400-2933800	Strong transcription	Fetal Brain Female	brain
17	chr4:2924400-2934200	Strong transcription	Brain Germinal Matrix	brain
18	chr4:2924600-2932600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:2924800-2933600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:2925000-2933800	Strong transcription	Dnd41	blood
21	chr4:2925000-2934400	Strong transcription	Osteobl	bone
22	chr4:2925200-2932600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr4:2925200-2932600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:2925200-2933200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:2925200-2933400	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr4:2925200-2934800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:2925400-2932800	Strong transcription	Primary T cells from cord blood	blood
28	chr4:2925400-2932800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:2925400-2933000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:2925400-2933200	Strong transcription	HSMMtube	muscle
31	chr4:2925400-2933400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:2925400-2934400	Strong transcription	NHLF	lung
33	chr4:2925600-2932800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:2925600-2932800	Strong transcription	GM12878-XiMat	blood
35	chr4:2925600-2933000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:2925600-2933000	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr4:2925600-2933000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:2925600-2933200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr4:2925600-2933800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:2925600-2934200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:2925600-2934400	Strong transcription	NHEK	skin
42	chr4:2925800-2933000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:2925800-2934200	Strong transcription	Esophagus	oesophagus
44	chr4:2925800-2935000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:2926000-2933200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:2926000-2933200	Strong transcription	Aorta	Aorta
47	chr4:2926000-2933600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:2926000-2934200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:2926000-2934400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:2926200-2933000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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