Variant report

Variant	rs12199089
Chromosome Location	chr6:1605504-1605505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1604255..1605544-chr6:2104014..2105193,5	K562	blood:
2	chr6:1605093..1609098-chr6:1671097..1673871,3	MCF-7	breast:
3	chr6:1599906..1601907-chr6:1602978..1605536,2	K562	blood:
4	chr6:1603725..1606000-chr6:2194697..2196437,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GMDS-6	chr6:1603265-1608466	NONHSAT106529
2	lnc-GMDS-6	chr6:1605088-1607351	NONHSAT106531

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv917248	chr6:1365437-1627813	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1034039	chr6:1427061-1691837	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv538088	chr6:1427061-1691837	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv1027393	chr6:1446300-1692019	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active 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	32 gene(s)	inside rSNPs	diseases
9	nsv538089	chr6:1446300-1692019	Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1016859	chr6:1460020-1645819	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv883376	chr6:1535043-1635082	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv1016594	chr6:1590030-1702529	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	nsv823394	chr6:1590091-1629146	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv883378	chr6:1593851-1623990	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	nsv883379	chr6:1593851-1628902	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
17	nsv823395	chr6:1595031-1629521	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
18	nsv883380	chr6:1595216-1621404	Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
19	nsv883381	chr6:1595216-1628902	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
20	nsv823396	chr6:1597359-1629106	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
21	nsv883382	chr6:1598942-1620037	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
22	esv3439668	chr6:1603778-1606326	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv823397	chr6:1603867-1622264	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers 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	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1604000-1605800	Bivalent Enhancer	Fetal Brain Male	brain
2	chr6:1604200-1605800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:1604200-1606000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:1604200-1610800	Active TSS	Aorta	Aorta
5	chr6:1604400-1605600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:1604400-1605600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr6:1604400-1605600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:1604400-1605600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
9	chr6:1604400-1605600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
10	chr6:1604400-1605800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:1604400-1605800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
12	chr6:1604400-1605800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:1604400-1605800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:1604400-1605800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:1604400-1606000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:1604400-1606000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
17	chr6:1604400-1606000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
18	chr6:1604400-1606000	Bivalent Enhancer	Placenta	Placenta
19	chr6:1604400-1606000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
20	chr6:1604400-1606200	Bivalent Enhancer	Fetal Stomach	stomach
21	chr6:1604400-1606400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:1604400-1610800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:1604600-1605600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
24	chr6:1604600-1605800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:1604600-1605800	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr6:1604600-1605800	Enhancers	Spleen	Spleen
27	chr6:1604800-1605600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
28	chr6:1604800-1605600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:1604800-1605600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:1604800-1605600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:1604800-1605600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
32	chr6:1604800-1605600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
33	chr6:1604800-1605600	Flanking Active TSS	Right Ventricle	heart
34	chr6:1604800-1605600	Flanking Bivalent TSS/Enh	Thymus	Thymus
35	chr6:1604800-1605800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
36	chr6:1604800-1605800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
37	chr6:1604800-1605800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:1604800-1605800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:1604800-1605800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
40	chr6:1604800-1605800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
41	chr6:1604800-1606000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
42	chr6:1604800-1609600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
43	chr6:1605000-1605600	Flanking Active TSS	Pancreas	Pancrea
44	chr6:1605000-1605600	Bivalent/Poised TSS	HepG2	liver
45	chr6:1605000-1606000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
46	chr6:1605000-1606000	Bivalent Enhancer	Small Intestine	intestine
47	chr6:1605000-1606200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:1605000-1606400	Bivalent Enhancer	Brain Germinal Matrix	brain
49	chr6:1605000-1606400	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr6:1605000-1607400	Bivalent Enhancer	GM12878-XiMat	blood

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