Variant report

Variant	rs12648696
Chromosome Location	chr4:103546896-103546897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103545322..103548006-chr4:103788328..103790591,2	MCF-7	breast:
2	chr4:103542281..103545235-chr4:103546204..103549504,3	K562	blood:
3	chr4:103370620..103371572-chr4:103546507..103547372,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109332	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000248161	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11722146	0.94[CHB][hapmap]
rs11723120	0.93[CHB][hapmap]
rs118882	0.89[CHB][hapmap]
rs12509517	0.94[CHB][hapmap]
rs1598859	0.94[CHB][hapmap]
rs1609798	0.94[CHB][hapmap]
rs170731	0.89[CHB][hapmap]
rs1801	0.94[CHB][hapmap]
rs227276	0.80[CHB][hapmap]
rs227277	0.80[CHB][hapmap]
rs228619	0.80[CHB][hapmap]
rs230491	0.89[CHB][hapmap]
rs230492	0.89[CHB][hapmap]
rs230493	0.89[CHB][hapmap]
rs230498	0.89[CHB][hapmap]
rs230500	0.89[CHB][hapmap]
rs230504	0.89[CHB][hapmap]
rs230509	0.89[CHB][hapmap]
rs230514	0.89[CHB][hapmap]
rs230515	0.86[CHB][hapmap]
rs230516	0.94[CHB][hapmap]
rs230519	0.89[CHB][hapmap]
rs230520	0.89[CHB][hapmap]
rs230525	0.89[CHB][hapmap]
rs230531	0.89[CHB][hapmap]
rs230532	0.89[CHB][hapmap]
rs230533	0.89[CHB][hapmap]
rs230534	0.88[CHB][hapmap]
rs230535	0.89[CHB][hapmap]
rs230539	0.94[CHB][hapmap]
rs230540	0.94[CHB][hapmap]
rs230542	0.94[CHB][hapmap]
rs3755867	0.94[CHB][hapmap]
rs3774959	0.94[CHB][hapmap]
rs3774963	0.94[CHB][hapmap]
rs4648055	0.94[CHB][hapmap]
rs4648068	0.94[CHB][hapmap]
rs4648133	0.94[CHB][hapmap]
rs4698858	0.81[JPT][hapmap]
rs4698861	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4698863	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7674640	0.88[CHB][hapmap]
rs9790601	0.94[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003618	chr4:103530465-103562161	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103521400-103554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:103536200-103552800	Weak transcription	Ovary	ovary
3	chr4:103536200-103595400	Weak transcription	Colonic Mucosa	Colon
4	chr4:103536400-103553400	Weak transcription	Fetal Brain Female	brain
5	chr4:103536600-103550800	Weak transcription	Thymus	Thymus
6	chr4:103536600-103562600	Weak transcription	Brain Germinal Matrix	brain
7	chr4:103536600-103595800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:103538000-103552800	Weak transcription	Spleen	Spleen
9	chr4:103538200-103549400	Weak transcription	Fetal Lung	lung
10	chr4:103538200-103550800	Weak transcription	Lung	lung
11	chr4:103538200-103552400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:103538200-103555600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:103538200-103555600	Weak transcription	Gastric	stomach
14	chr4:103538200-103555800	Weak transcription	Esophagus	oesophagus
15	chr4:103538600-103552800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:103538800-103552800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr4:103538800-103552800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:103538800-103552800	Weak transcription	Adipose Nuclei	Adipose
19	chr4:103538800-103555600	Weak transcription	Right Ventricle	heart
20	chr4:103538800-103555800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:103541800-103562400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:103541800-103571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:103542000-103547400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:103542000-103552400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:103542200-103552000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr4:103542200-103552800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:103542200-103552800	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:103542200-103552800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr4:103542200-103555400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:103542200-103555400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:103542200-103555600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr4:103542200-103555600	Weak transcription	Brain Anterior Caudate	brain
33	chr4:103542400-103549000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:103542400-103552800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:103542400-103552800	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:103542400-103552800	Weak transcription	Left Ventricle	heart
37	chr4:103542400-103553200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:103542400-103555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:103542400-103555600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:103542400-103557200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:103542400-103560800	Weak transcription	Brain Substantia Nigra	brain
42	chr4:103542400-103562200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:103542400-103578800	Weak transcription	Psoas Muscle	Psoas
44	chr4:103542400-103594400	Weak transcription	K562	blood
45	chr4:103542400-103617400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr4:103542600-103555800	Weak transcription	Brain Hippocampus Middle	brain
47	chr4:103542800-103548000	Weak transcription	HMEC	breast
48	chr4:103542800-103548600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:103542800-103548600	Weak transcription	NHLF	lung
50	chr4:103542800-103549400	Weak transcription	Fetal Heart	heart

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