Variant report

Variant	rs2571375
Chromosome Location	chr6:29945270-29945271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29855991..29858588-chr6:29944087..29945954,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HLA-A-1	chr6:29945244-29945280	ENSG00000204625

Variant related genes	Relation type
ENSG00000230521	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1150738	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17180241	0.83[EUR][1000 genomes]
rs2256902	0.83[EUR][1000 genomes]
rs2523961	0.83[EUR][1000 genomes]
rs259949	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	esv1845786	chr6:29817123-29955129	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1848127	chr6:29817323-29966451	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	esv3369212	chr6:29827361-29960177	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	esv2757159	chr6:29834472-29965501	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	esv3376588	chr6:29834667-29964324	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv10810	chr6:29837465-29961415	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv870444	chr6:29842885-29949545	Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription 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	57 gene(s)	inside rSNPs	diseases
21	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
22	esv1799283	chr6:29938777-29959935	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	esv3350882	chr6:29942373-29945471	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29942600-29945400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:29942600-29945400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:29942800-29945400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:29943200-29945400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
5	chr6:29943200-29945400	Active TSS	Psoas Muscle	Psoas
6	chr6:29944000-29945400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:29944000-29945400	Active TSS	Brain Angular Gyrus	brain
8	chr6:29944000-29945400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:29944000-29945400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:29944000-29945400	Active TSS	Colon Smooth Muscle	Colon
11	chr6:29944000-29945400	Active TSS	Right Atrium	heart
12	chr6:29944000-29945400	Flanking Active TSS	HMEC	breast
13	chr6:29944000-29945400	Active TSS	HSMM	muscle
14	chr6:29944000-29945400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr6:29944200-29945400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
16	chr6:29944200-29945400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:29944200-29945400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:29944200-29945400	Active TSS	Rectal Smooth Muscle	rectum
19	chr6:29944200-29945400	Active TSS	NHDF-Ad	bronchial
20	chr6:29944200-29945600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr6:29944400-29945400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr6:29944400-29945400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:29944400-29945400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
24	chr6:29944400-29945400	Active TSS	Brain Substantia Nigra	brain
25	chr6:29944400-29945400	Bivalent/Poised TSS	Fetal Stomach	stomach
26	chr6:29944400-29945400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:29944400-29945400	Active TSS	HSMMtube	muscle
28	chr6:29944400-29945400	Bivalent/Poised TSS	NHEK	skin
29	chr6:29944400-29945400	Active TSS	NHLF	lung
30	chr6:29944400-29945600	Active TSS	Brain Anterior Caudate	brain
31	chr6:29944400-29945600	Active TSS	Stomach Smooth Muscle	stomach
32	chr6:29944600-29945400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:29944800-29945400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
34	chr6:29944800-29945400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:29944800-29945400	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr6:29944800-29945400	Active TSS	Fetal Kidney	kidney
37	chr6:29945000-29945400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr6:29945000-29945400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:29945000-29945400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr6:29945000-29945400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:29945000-29945400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr6:29945000-29945400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:29945000-29945400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr6:29945000-29945400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:29945000-29945400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:29945000-29945400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:29945000-29945400	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr6:29945000-29945400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
49	chr6:29945000-29945400	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr6:29945000-29945400	Flanking Active TSS	Fetal Intestine Small	intestine

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