Variant report

Variant	rs12441499
Chromosome Location	chr15:75164978-75164979
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75163746..75165751-chr15:75191304..75195509,4	K562	blood:
2	chr15:75162469..75167536-chr15:75180880..75184902,6	K562	blood:
3	chr15:75164429..75167842-chr15:75196018..75198435,3	K562	blood:
4	chr15:75163901..75170368-chr15:75180139..75184021,10	K562	blood:
5	chr15:75163277..75165219-chr15:75166368..75168466,2	MCF-7	breast:
6	chr15:75129767..75136088-chr15:75163908..75167881,8	K562	blood:
7	chr15:75134049..75139648-chr15:75161531..75167020,13	MCF-7	breast:
8	chr15:75163895..75166026-chr15:75315159..75317542,2	MCF-7	breast:
9	chr15:75073135..75075746-chr15:75163972..75165852,2	K562	blood:
10	chr15:75163351..75167012-chr15:75180238..75185061,13	MCF-7	breast:
11	chr15:75163342..75166719-chr15:75180364..75184673,7	MCF-7	breast:
12	chr15:75161914..75167776-chr15:75191644..75199761,13	MCF-7	breast:
13	chr15:75164573..75166914-chr15:75228746..75230664,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000140474	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000260824	Chromatin interaction
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11072511	0.95[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs1130741	0.95[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs11857695	0.83[AFR][1000 genomes]
rs12101507	0.85[AFR][1000 genomes]
rs12439641	1.00[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12440159	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs12442804	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12902515	0.86[AFR][1000 genomes]
rs12903205	0.83[AFR][1000 genomes]
rs12904897	0.80[AFR][1000 genomes]
rs12913293	0.86[AFR][1000 genomes]
rs2230479	0.85[LWK][hapmap];0.82[AFR][1000 genomes]
rs28726277	0.86[AFR][1000 genomes]
rs3935818	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4886635	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs4886636	0.90[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs56671860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58856253	0.87[AFR][1000 genomes]
rs60494786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60698434	0.85[AFR][1000 genomes]
rs7179093	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs729263	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7495739	0.95[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs8025447	0.84[AFR][1000 genomes]
rs8031052	0.81[AFR][1000 genomes]
rs8032473	0.94[AFR][1000 genomes]
rs9672491	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv827386	chr15:75161362-75166473	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a
4	nsv827388	chr15:75161362-75169121	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75158000-75165000	Enhancers	Spleen	Spleen
2	chr15:75158200-75165000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:75161600-75165400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:75163600-75165000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:75163800-75166000	Active TSS	GM12878-XiMat	blood
6	chr15:75164200-75165200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr15:75164200-75165200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:75164200-75165400	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr15:75164200-75166000	Active TSS	Stomach Smooth Muscle	stomach
10	chr15:75164200-75166400	Active TSS	Rectal Smooth Muscle	rectum
11	chr15:75164400-75165000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr15:75164400-75165200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr15:75164400-75165200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:75164400-75165200	Flanking Active TSS	Dnd41	blood
15	chr15:75164400-75165400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr15:75164400-75165400	Flanking Active TSS	Placenta	Placenta
17	chr15:75164400-75165400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr15:75164400-75166400	Active TSS	HSMMtube	muscle
19	chr15:75164600-75165000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:75164600-75165000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:75164600-75165000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr15:75164600-75165000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:75164600-75165000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr15:75164600-75165000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:75164600-75165000	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr15:75164600-75165000	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr15:75164600-75165000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:75164600-75165000	Flanking Active TSS	Brain Substantia Nigra	brain
29	chr15:75164600-75165000	Flanking Active TSS	Colonic Mucosa	Colon
30	chr15:75164600-75165000	Flanking Active TSS	Fetal Intestine Small	intestine
31	chr15:75164600-75165000	Flanking Active TSS	Pancreas	Pancrea
32	chr15:75164600-75165000	Enhancers	Placenta Amnion	Placenta Amnion
33	chr15:75164600-75165000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr15:75164600-75165000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr15:75164600-75165000	Flanking Active TSS	Right Ventricle	heart
36	chr15:75164600-75165000	Flanking Active TSS	HepG2	liver
37	chr15:75164600-75165200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:75164600-75165200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr15:75164600-75165200	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr15:75164600-75165200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr15:75164600-75165200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:75164600-75165200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr15:75164600-75165200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:75164600-75165200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:75164600-75165200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:75164600-75165200	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr15:75164600-75165200	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr15:75164600-75165200	Flanking Active TSS	Fetal Brain Male	brain
49	chr15:75164600-75165200	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr15:75164600-75165200	Flanking Active TSS	Thymus	Thymus

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