Variant report

Variant	rs41329644
Chromosome Location	chr4:3314287-3314288
allele	C/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	POLR2A	chr4:3314243-3314436	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3312095..3315185-chr4:3316131..3319628,4	MCF-7	breast:
2	chr4:3313691..3315638-chr4:3318418..3320461,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C4orf44-4	chr4:3314239-3314562	NONHSAT094860

Variant related genes	Relation type
ENSG00000248840	TF binding region
RGS12	TF binding region
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16843858	1.00[MEX][hapmap]
rs16844136	1.00[CEU][hapmap]
rs16844163	1.00[CEU][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs16844166	1.00[CEU][hapmap]
rs16844169	1.00[CEU][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs16844176	1.00[CEU][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs16844191	1.00[MEX][hapmap]
rs16844223	1.00[CEU][hapmap]
rs16844251	1.00[MEX][hapmap]
rs16844335	1.00[CEU][hapmap]
rs16844398	1.00[CEU][hapmap]
rs41347150	1.00[CEU][hapmap]
rs6826787	1.00[CEU][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs7679941	1.00[MEX][hapmap]
rs7690736	1.00[MEX][hapmap]
rs7691619	1.00[CEU][hapmap]
rs9291160	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
5	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv966506	chr4:3308550-3320391	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3296600-3318600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:3299600-3318600	Weak transcription	Aorta	Aorta
3	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:3304800-3318600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:3306600-3320600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:3307000-3320600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:3307200-3318000	Weak transcription	Liver	Liver
8	chr4:3307200-3327000	Weak transcription	Fetal Kidney	kidney
9	chr4:3307400-3325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:3307400-3326800	Weak transcription	A549	lung
11	chr4:3307600-3315000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:3307600-3322200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:3307600-3323000	Weak transcription	NH-A	brain
14	chr4:3307600-3323600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:3307800-3319000	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:3308000-3318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:3308000-3318600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:3308000-3319800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:3308000-3322800	Weak transcription	NHDF-Ad	bronchial
20	chr4:3308000-3323600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:3308000-3323800	Weak transcription	Osteobl	bone
22	chr4:3308000-3326000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:3308000-3327000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:3308200-3314400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:3308200-3318400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:3308200-3318400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:3308200-3318600	Weak transcription	NHLF	lung
28	chr4:3308200-3319800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:3308200-3320400	Weak transcription	Fetal Heart	heart
30	chr4:3308200-3323200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:3308400-3315000	Weak transcription	Primary T cells from cord blood	blood
32	chr4:3308400-3317800	Weak transcription	HSMM	muscle
33	chr4:3308400-3318200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:3308400-3318200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:3308400-3320200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:3308400-3321400	Weak transcription	Stomach Mucosa	stomach
37	chr4:3308600-3317400	Weak transcription	Pancreas	Pancrea
38	chr4:3308600-3317800	Weak transcription	Adipose Nuclei	Adipose
39	chr4:3308600-3317800	Weak transcription	Left Ventricle	heart
40	chr4:3308600-3318000	Weak transcription	HSMMtube	muscle
41	chr4:3308600-3318200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:3308600-3319000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:3308600-3319400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:3308600-3322600	Weak transcription	Brain Substantia Nigra	brain
45	chr4:3308600-3323000	Weak transcription	Brain Angular Gyrus	brain
46	chr4:3309000-3318000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:3309000-3322000	Weak transcription	Right Atrium	heart
48	chr4:3309000-3327200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr4:3309200-3316600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:3309600-3319000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links