Variant report

Variant	rs11962999
Chromosome Location	chr6:74276935-74276936
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74227750..74233305-chr6:74272676..74276952,12	K562	blood:
2	chr6:74225495..74228323-chr6:74275867..74278333,2	MCF-7	breast:
3	chr6:74270566..74272311-chr6:74274568..74277117,2	K562	blood:
4	chr6:74274687..74279711-chr6:74293912..74296161,4	K562	blood:
5	chr6:74273534..74278713-chr6:74287099..74290342,5	K562	blood:
6	chr6:74231699..74233989-chr6:74275538..74278472,2	MCF-7	breast:
7	chr6:74275602..74279787-chr6:74300038..74304050,3	MCF-7	breast:
8	chr6:74227140..74235678-chr6:74271460..74282263,27	K562	blood:
9	chr6:74273534..74277710-chr6:74287099..74290160,5	K562	blood:
10	chr6:74229153..74233317-chr6:74274374..74277144,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229862	Chromatin interaction
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10498892	0.86[EUR][1000 genomes]
rs11962336	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11964414	0.84[EUR][1000 genomes]
rs12191042	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12191488	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12195584	0.86[EUR][1000 genomes]
rs12197318	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12197927	0.83[EUR][1000 genomes]
rs12199577	0.90[JPT][hapmap]
rs12200338	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12211279	0.83[EUR][1000 genomes]
rs12212297	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13203297	0.80[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34613232	0.83[EUR][1000 genomes]
rs35256309	0.86[EUR][1000 genomes]
rs35659919	0.97[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3857465	0.89[JPT][hapmap]
rs4708064	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];0.96[ASN][1000 genomes]

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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	esv2763576	chr6:74197638-74277249	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
9	nsv463153	chr6:74229258-74290291	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
10	nsv603693	chr6:74229258-74290291	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
11	nsv527357	chr6:74253266-74325403	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv603694	chr6:74275405-74365807	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74274200-74277400	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr6:74274600-74277000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:74274600-74277400	Enhancers	HSMMtube	muscle
4	chr6:74274600-74278600	Enhancers	Placenta	Placenta
5	chr6:74274800-74277000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:74275000-74277000	Enhancers	Liver	Liver
7	chr6:74275000-74277200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:74275000-74277600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr6:74275000-74277600	Enhancers	Fetal Intestine Small	intestine
10	chr6:74275000-74278400	Enhancers	Fetal Intestine Large	intestine
11	chr6:74275200-74277200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr6:74275200-74277200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr6:74275200-74277200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:74275200-74277200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:74275200-74277200	Enhancers	HSMM	muscle
16	chr6:74275200-74277400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:74275200-74277400	Enhancers	Osteobl	bone
18	chr6:74275200-74277600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:74275400-74277000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:74275400-74277200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:74275400-74277200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:74275400-74277200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:74275400-74277200	Enhancers	NH-A	brain
24	chr6:74275400-74277400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr6:74275400-74277600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:74275400-74278200	Enhancers	NHDF-Ad	bronchial
27	chr6:74275600-74277000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:74275600-74277400	Flanking Active TSS	HepG2	liver
29	chr6:74275800-74277200	Enhancers	HMEC	breast
30	chr6:74275800-74277200	Enhancers	NHEK	skin
31	chr6:74276000-74277200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:74276000-74277400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:74276000-74277400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr6:74276000-74277600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr6:74276000-74277600	Enhancers	Stomach Mucosa	stomach
36	chr6:74276000-74279200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr6:74276200-74277000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr6:74276200-74277000	Weak transcription	NHLF	lung
39	chr6:74276200-74277400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:74276200-74277400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:74276400-74277000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:74276400-74277200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr6:74276400-74277400	Enhancers	Pancreas	Pancrea
44	chr6:74276400-74280200	Weak transcription	Fetal Heart	heart
45	chr6:74276400-74287800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:74276600-74277000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr6:74276600-74277000	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr6:74276600-74277000	Active TSS	A549	lung
49	chr6:74276600-74277000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr6:74276600-74277200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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