Variant report

Variant	rs61139307
Chromosome Location	chr2:39039228-39039229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38977082..38978650-chr2:39037995..39040389,2	K562	blood:
2	chr2:39004566..39006965-chr2:39038166..39040437,2	MCF-7	breast:
3	chr2:38977150..38978666-chr2:39038889..39040421,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GEMIN6-1	chr2:39038701-39040716	predAs_engstrom06_BX108565_1

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11888905	1.00[AMR][1000 genomes]
rs11892292	1.00[AMR][1000 genomes]
rs11894209	1.00[AMR][1000 genomes]
rs11899756	1.00[AMR][1000 genomes]
rs4592827	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55809581	1.00[AMR][1000 genomes]
rs56239346	1.00[AMR][1000 genomes]
rs56407729	1.00[AMR][1000 genomes]
rs58080550	1.00[AMR][1000 genomes]
rs58449189	1.00[AMR][1000 genomes]
rs59364009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59983786	1.00[AMR][1000 genomes]
rs60895887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61556896	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6708518	1.00[AMR][1000 genomes]
rs6724203	1.00[AMR][1000 genomes]
rs6756998	1.00[AMR][1000 genomes]
rs73930361	1.00[AMR][1000 genomes]
rs73930365	1.00[AMR][1000 genomes]
rs73930366	1.00[AMR][1000 genomes]
rs73930371	1.00[AMR][1000 genomes]
rs73930376	1.00[AMR][1000 genomes]
rs73930385	1.00[AMR][1000 genomes]
rs73930386	1.00[AMR][1000 genomes]
rs73930394	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 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	chr2:39006400-39045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:39009200-39042600	Weak transcription	Fetal Kidney	kidney
4	chr2:39009200-39050000	Weak transcription	HMEC	breast
5	chr2:39009200-39052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:39017600-39042200	Weak transcription	Small Intestine	intestine
7	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:39022000-39042600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
10	chr2:39024000-39053000	Weak transcription	Psoas Muscle	Psoas
11	chr2:39025600-39042400	Weak transcription	Hela-S3	cervix
12	chr2:39025600-39042400	Weak transcription	HSMM	muscle
13	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:39030000-39040800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
16	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:39033000-39041400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:39033000-39053000	Weak transcription	Fetal Brain Male	brain
19	chr2:39033800-39050200	Weak transcription	K562	blood
20	chr2:39034200-39041400	Weak transcription	GM12878-XiMat	blood
21	chr2:39036000-39046800	Strong transcription	Fetal Stomach	stomach
22	chr2:39036000-39054000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:39036200-39039800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:39036200-39043800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:39036400-39051600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:39037000-39046000	Strong transcription	Fetal Intestine Small	intestine
27	chr2:39037000-39046800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:39037200-39040200	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:39037200-39055800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:39037400-39039600	Strong transcription	Brain Anterior Caudate	brain
31	chr2:39037400-39040000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:39037400-39040000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr2:39037400-39041200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:39037400-39041400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:39037400-39041400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr2:39037400-39041600	Strong transcription	Placenta	Placenta
37	chr2:39037400-39043200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:39037400-39046000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:39037400-39046600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:39037400-39046600	Strong transcription	Fetal Brain Female	brain
41	chr2:39037400-39046800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr2:39037400-39047200	Strong transcription	Primary T cells from cord blood	blood
43	chr2:39037400-39047800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:39037400-39047800	Strong transcription	Left Ventricle	heart
45	chr2:39037400-39052000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:39037400-39054000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:39037400-39054000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:39037400-39054600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:39037600-39039400	Strong transcription	Osteobl	bone
50	chr2:39037600-39039600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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