Variant report

Variant	rs213239
Chromosome Location	chr6:28318481-28318482
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28247642..28250446-chr6:28317779..28319288,2	K562	blood:
2	chr6:28249255..28252885-chr6:28315781..28319284,4	K562	blood:
3	chr6:28247366..28250224-chr6:28317764..28319401,2	MCF-7	breast:
4	chr6:28318312..28320612-chr6:28351068..28352730,2	K562	blood:
5	chr6:28103114..28106211-chr6:28315199..28319125,3	K562	blood:
6	chr6:28314766..28319001-chr6:28320941..28324187,4	MCF-7	breast:
7	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
8	chr6:28127970..28130555-chr6:28316475..28318965,2	K562	blood:
9	chr6:28192912..28194626-chr6:28318304..28321178,2	MCF-7	breast:
10	chr6:27636377..27638707-chr6:28318162..28320333,2	K562	blood:
11	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
12	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
13	chr6:28218194..28221046-chr6:28316270..28319035,4	K562	blood:
14	chr6:28219546..28223731-chr6:28316147..28319107,5	K562	blood:
15	chr6:28101857..28106060-chr6:28315199..28321034,6	K562	blood:
16	chr6:28315597..28319153-chr6:28366055..28369015,3	K562	blood:
17	chr6:28317772..28319708-chr6:28509467..28511768,2	K562	blood:
18	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000187626	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000137338	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10456362	1.00[JPT][hapmap]
rs1076639	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11751487	0.80[ASN][1000 genomes]
rs11755032	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11755387	0.82[CHB][hapmap]
rs11965538	1.00[JPT][hapmap]
rs13200462	1.00[JPT][hapmap]
rs1339899	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1419183	1.00[JPT][hapmap]
rs1679709	1.00[JPT][hapmap]
rs1679732	1.00[JPT][hapmap]
rs16893735	0.82[CEU][hapmap]
rs16894011	0.81[CHB][hapmap];0.88[YRI][hapmap]
rs1778507	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1778508	1.00[JPT][hapmap]
rs1778511	1.00[JPT][hapmap]
rs17856167	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[YRI][hapmap]
rs1936365	1.00[JPT][hapmap]
rs2108926	0.81[YRI][hapmap]
rs213241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs213244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232427	0.82[CHB][hapmap]
rs2743554	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2799077	1.00[JPT][hapmap]
rs2799079	0.81[CHB][hapmap]
rs6901575	1.00[JPT][hapmap]
rs6920512	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs6942030	0.81[YRI][hapmap]
rs73742521	0.89[EUR][1000 genomes]
rs853676	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs853678	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs853679	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs853681	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs853682	0.83[ASN][1000 genomes]
rs853685	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs853687	0.85[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853688	0.87[ASN][1000 genomes]
rs853694	0.82[ASN][1000 genomes]
rs9295765	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs9366717	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs9393908	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs9461446	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9461448	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461449	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468321	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9468322	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9468342	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468345	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468364	0.81[CHB][hapmap];0.84[YRI][hapmap];0.82[AMR][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28317000-28318800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:28317000-28319000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:28317000-28319000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:28317200-28318600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:28317200-28318600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr6:28317200-28318600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:28317200-28318600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:28317200-28318600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28317200-28318600	Active TSS	Brain Anterior Caudate	brain
10	chr6:28317200-28318600	Active TSS	Fetal Intestine Small	intestine
11	chr6:28317200-28318600	Active TSS	Placenta Amnion	Placenta Amnion
12	chr6:28317200-28318600	Active TSS	GM12878-XiMat	blood
13	chr6:28317200-28318600	Active TSS	NHDF-Ad	bronchial
14	chr6:28317200-28318800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:28317200-28318800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:28317200-28318800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:28317200-28318800	Active TSS	Brain Cingulate Gyrus	brain
18	chr6:28317200-28318800	Active TSS	Colonic Mucosa	Colon
19	chr6:28317200-28318800	Active TSS	Fetal Stomach	stomach
20	chr6:28317200-28318800	Active TSS	Ovary	ovary
21	chr6:28317200-28319000	Active TSS	H1 Cell Line	embryonic stem cell
22	chr6:28317200-28319000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:28317200-28319000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:28317200-28319000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:28317200-28319000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:28317200-28319000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:28317200-28319000	Active TSS	HSMMtube	muscle
28	chr6:28317200-28319000	Active TSS	K562	blood
29	chr6:28317200-28319000	Active TSS	NHLF	lung
30	chr6:28317200-28319200	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr6:28317200-28319200	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr6:28317200-28319400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:28317200-28319400	Active TSS	Right Atrium	heart
34	chr6:28317200-28319600	Active TSS	HSMM	muscle
35	chr6:28317200-28322000	Active TSS	Rectal Smooth Muscle	rectum
36	chr6:28317200-28322200	Active TSS	Stomach Smooth Muscle	stomach
37	chr6:28317400-28318600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:28318000-28318600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:28318000-28318600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr6:28318000-28318800	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr6:28318000-28318800	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr6:28318000-28318800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr6:28318000-28318800	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr6:28318000-28318800	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr6:28318000-28319200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:28318000-28319200	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr6:28318000-28319400	Flanking Active TSS	Liver	Liver
48	chr6:28318000-28319400	Flanking Active TSS	Dnd41	blood
49	chr6:28318000-28319600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:28318200-28318600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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