Variant report

Variant	rs11934628
Chromosome Location	chr4:77120369-77120370
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	MTA3	chr4:77119043-77120433	GM12878	blood:	n/a	n/a
2	STAT5A	chr4:77118944-77120379	GM12878	blood:	n/a	chr4:77119309-77119317
3	ATF2	chr4:77118690-77120437	GM12878	blood:	n/a	n/a
4	RUNX3	chr4:77118965-77120372	GM12878	blood:	n/a	n/a
5	CREB1	chr4:77119463-77120394	GM12878	blood:	n/a	n/a
6	ATF2	chr4:77119476-77121237	GM12878	blood:	n/a	n/a
7	NRF1	chr4:77120281-77120389	GM12878	blood:	n/a	n/a
8	NFATC1	chr4:77119084-77120416	GM12878	blood:	n/a	n/a
9	EP300	chr4:77119136-77121422	GM12878	blood:	n/a	chr4:77120044-77120058
10	CHD1	chr4:77119329-77121096	GM12878	blood:	n/a	n/a
11	NFIC	chr4:77118966-77120404	GM12878	blood:	n/a	chr4:77119704-77119721 chr4:77119704-77119720
12	TCF12	chr4:77119542-77120436	GM12878	blood:	n/a	n/a
13	FOXM1	chr4:77119109-77120394	GM12878	blood:	n/a	n/a
14	BHLHE40	chr4:77119061-77120469	GM12878	blood:	n/a	chr4:77119972-77119981 chr4:77119970-77119983 chr4:77119972-77119981
15	TCF3	chr4:77119413-77120521	GM12878	blood:	n/a	n/a
16	CHD2	chr4:77119087-77120373	GM12878	blood:	n/a	n/a
17	YY1	chr4:77120013-77120526	GM12878	blood:	n/a	n/a
18	FOXM1	chr4:77118999-77121516	GM12878	blood:	n/a	n/a
19	NFIC	chr4:77118950-77121515	GM12878	blood:	n/a	chr4:77119704-77119721 chr4:77119704-77119720
20	TCF3	chr4:77119605-77120443	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:77118780..77124053-chr4:77134347..77137767,5	MCF-7	breast:
2	chr4:77118894..77122374-chr4:77129647..77132337,3	K562	blood:
3	chr4:77114541..77118897-chr4:77119397..77123368,6	K562	blood:
4	chr4:77118497..77121388-chr4:77227077..77230082,4	MCF-7	breast:
5	chr4:77119760..77123050-chr4:77133589..77135332,3	K562	blood:

Variant related genes	Relation type
SCARB2	TF binding region
ENSG00000189157	Chromatin interaction
ENSG00000138760	Chromatin interaction
ENSG00000118804	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11938219	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11941285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11944780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001553	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001556	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001644	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001645	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001647	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001648	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17001649	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2228380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28655570	1.00[EUR][1000 genomes]
rs34078946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34647444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34865218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35211143	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35634209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35866970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4129291	1.00[AMR][1000 genomes]
rs56891967	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58990415	1.00[EUR][1000 genomes]
rs59199771	1.00[EUR][1000 genomes]
rs59815580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59876319	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60319873	1.00[EUR][1000 genomes]
rs60541751	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60744184	1.00[EUR][1000 genomes]
rs61079077	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61313750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6832579	1.00[EUR][1000 genomes]
rs7672121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs999358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs999359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799666	chr4:77119942-77129568	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77113200-77134000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:77113600-77134200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:77114200-77122400	Enhancers	Right Ventricle	heart
4	chr4:77114600-77121000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:77114600-77122000	Enhancers	HMEC	breast
6	chr4:77114800-77122800	Enhancers	Psoas Muscle	Psoas
7	chr4:77115200-77122200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:77115400-77122600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:77115600-77120800	Enhancers	Adipose Nuclei	Adipose
10	chr4:77116200-77122400	Enhancers	Pancreas	Pancrea
11	chr4:77116200-77122400	Enhancers	Right Atrium	heart
12	chr4:77116600-77122600	Enhancers	Fetal Thymus	thymus
13	chr4:77116800-77122200	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:77117000-77122800	Enhancers	Small Intestine	intestine
15	chr4:77117000-77134000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:77117200-77121400	Enhancers	Spleen	Spleen
17	chr4:77117200-77129200	Enhancers	Liver	Liver
18	chr4:77117400-77122600	Enhancers	Thymus	Thymus
19	chr4:77117400-77132800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:77117600-77121000	Enhancers	Primary hematopoietic stem cells	blood
21	chr4:77117800-77122200	Enhancers	NHDF-Ad	bronchial
22	chr4:77117800-77122400	Enhancers	Left Ventricle	heart
23	chr4:77117800-77122800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:77118000-77120400	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr4:77118000-77120400	Flanking Active TSS	GM12878-XiMat	blood
26	chr4:77118000-77121400	Enhancers	Aorta	Aorta
27	chr4:77118000-77122000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr4:77118000-77122400	Enhancers	Fetal Heart	heart
29	chr4:77118200-77120400	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr4:77118200-77121000	Enhancers	Primary B cells from cord blood	blood
31	chr4:77118200-77121600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr4:77118200-77122600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr4:77118400-77120400	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr4:77118400-77121800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:77118400-77122000	Enhancers	Primary T cells from cord blood	blood
36	chr4:77118600-77121000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:77118600-77121200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:77118600-77121200	Enhancers	Fetal Muscle Trunk	muscle
39	chr4:77118600-77121800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr4:77118600-77122400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr4:77118800-77120400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:77118800-77120800	Enhancers	Fetal Intestine Small	intestine
43	chr4:77118800-77120800	Weak transcription	Ovary	ovary
44	chr4:77118800-77121800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr4:77118800-77122000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr4:77118800-77122200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:77118800-77122400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr4:77118800-77122400	Enhancers	Fetal Stomach	stomach
49	chr4:77118800-77122600	Enhancers	Fetal Muscle Leg	muscle
50	chr4:77118800-77123000	Enhancers	Stomach Mucosa	stomach

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