Variant report

Variant	rs3799261
Chromosome Location	chr6:53516779-53516780
allele	A/G
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:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:53357479..53358737-chr6:53515584..53517413,9	MCF-7	breast:
2	chr6:52969103..52972023-chr6:53515306..53517001,2	MCF-7	breast:
3	chr6:53406479..53414632-chr6:53513546..53521270,30	MCF-7	breast:
4	chr6:53329910..53332848-chr6:53516308..53518260,2	MCF-7	breast:
5	chr6:53515747..53517270-chr6:53543962..53544821,4	MCF-7	breast:
6	chr6:53516477..53518665-chr6:53518733..53520732,2	MCF-7	breast:
7	chr6:53408644..53409963-chr6:53515676..53516965,7	MCF-7	breast:
8	chr6:53516671..53518665-chr6:53582679..53584844,2	MCF-7	breast:
9	chr6:53376588..53381595-chr6:53515006..53518758,7	MCF-7	breast:
10	chr6:53357349..53358369-chr6:53515719..53517065,4	MCF-7	breast:
11	chr6:53514760..53518734-chr6:53657056..53660010,3	MCF-7	breast:
12	chr6:53399179..53403764-chr6:53515381..53518433,5	MCF-7	breast:
13	chr6:53433484..53436174-chr6:53515998..53518025,2	MCF-7	breast:
14	chr6:53408603..53410008-chr6:53515662..53517820,11	MCF-7	breast:
15	chr6:53358128..53360202-chr6:53515826..53517989,2	MCF-7	breast:
16	chr6:53408993..53409627-chr6:53516041..53516881,2	Hela-S3	cervix:
17	chr6:53515745..53518074-chr6:53571388..53574212,2	MCF-7	breast:
18	chr6:53411586..53414628-chr6:53512277..53518048,10	MCF-7	breast:
19	chr6:53363720..53366574-chr6:53515454..53517986,2	MCF-7	breast:
20	chr17:41438284..41438954-chr6:53516254..53516964,2	Hela-S3	cervix:
21	chr6:53516373..53518187-chr6:53597538..53600553,4	MCF-7	breast:
22	chr6:53406776..53411375-chr6:53513148..53518793,10	MCF-7	breast:
23	chr6:53500059..53502986-chr6:53515350..53517831,2	MCF-7	breast:
24	chr6:53486378..53488159-chr6:53514916..53516834,2	MCF-7	breast:
25	chr6:53516385..53519539-chr6:53524260..53526796,3	MCF-7	breast:
26	chr6:53516494..53516995-chr6:53819555..53820055,2	Hela-S3	cervix:
27	chr6:53516166..53518052-chr6:53518194..53521273,4	MCF-7	breast:
28	chr6:53514940..53517631-chr6:53536558..53538631,2	MCF-7	breast:
29	chr6:53515494..53519141-chr6:53521531..53524156,3	MCF-7	breast:
30	chr6:53515225..53517750-chr6:53793720..53795851,2	MCF-7	breast:
31	chr6:53476185..53479123-chr6:53515603..53517517,3	MCF-7	breast:
32	chr16:89894949..89895549-chr6:53516375..53516883,2	Hela-S3	cervix:
33	chr6:53515403..53517859-chr6:53544407..53545991,2	MCF-7	breast:
34	chr6:53363926..53366807-chr6:53516491..53518030,2	MCF-7	breast:
35	chr6:53384752..53385668-chr6:53516062..53516888,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000146147	Chromatin interaction
ENSG00000204991	Chromatin interaction
ENSG00000124743	Chromatin interaction
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction
ENSG00000001084	Chromatin interaction
ENSG00000236740	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs4476827	1.00[JPT][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53515600-53517400	Active TSS	Brain Cingulate Gyrus	brain
2	chr6:53515600-53517800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:53515800-53517000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:53515800-53517000	Active TSS	NHEK	skin
5	chr6:53515800-53517200	Active TSS	A549	lung
6	chr6:53515800-53517400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:53516000-53516800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:53516000-53517000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr6:53516000-53517000	Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr6:53516000-53517000	Active TSS	Hela-S3	cervix
11	chr6:53516000-53517200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:53516000-53517200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr6:53516000-53517400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:53516000-53517600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:53516200-53516800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:53516200-53516800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:53516200-53516800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr6:53516200-53516800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:53516200-53516800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr6:53516200-53516800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:53516200-53516800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:53516200-53516800	Active TSS	Fetal Kidney	kidney
23	chr6:53516200-53516800	Flanking Active TSS	Fetal Thymus	thymus
24	chr6:53516200-53516800	Flanking Active TSS	NH-A	brain
25	chr6:53516200-53516800	Active TSS	NHDF-Ad	bronchial
26	chr6:53516200-53516800	Flanking Active TSS	Osteobl	bone
27	chr6:53516200-53517000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr6:53516200-53517000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:53516200-53517000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:53516200-53517000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr6:53516200-53517000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:53516200-53517000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr6:53516200-53517000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr6:53516200-53517000	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr6:53516200-53517000	Active TSS	Primary T cells fromperipheralblood	blood
36	chr6:53516200-53517000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr6:53516200-53517000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:53516200-53517000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:53516200-53517000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:53516200-53517000	Active TSS	Aorta	Aorta
41	chr6:53516200-53517000	Active TSS	Brain Angular Gyrus	brain
42	chr6:53516200-53517000	Active TSS	Brain Anterior Caudate	brain
43	chr6:53516200-53517000	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr6:53516200-53517000	Active TSS	Brain Substantia Nigra	brain
45	chr6:53516200-53517000	Active TSS	Colon Smooth Muscle	Colon
46	chr6:53516200-53517000	Active TSS	Fetal Intestine Small	intestine
47	chr6:53516200-53517000	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr6:53516200-53517000	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr6:53516200-53517000	Bivalent/Poised TSS	Thymus	Thymus
50	chr6:53516200-53517000	Active TSS	HSMMtube	muscle

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