Variant report

Variant	rs12139411
Chromosome Location	chr1:160653567-160653568
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLAMF7-2	chr1:160653389-160653612	ENSG00000228863.4
2	lnc-SLAMF7-2	chr1:160653389-160653612	ENSG00000228863.1
3	lnc-SLAMF7-2	chr1:160653389-160653698	ENSG00000228863.4

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7527943	0.89[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	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv437213	chr1:160652730-160681836	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160643400-160655200	Weak transcription	Colonic Mucosa	Colon
2	chr1:160644600-160655800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:160645800-160653600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:160650400-160655600	Genic enhancers	Fetal Thymus	thymus
5	chr1:160650600-160656400	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr1:160650800-160655200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:160651000-160656400	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr1:160651000-160656400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:160651200-160655000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:160651200-160655800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:160651400-160656000	Genic enhancers	Primary B cells from cord blood	blood
12	chr1:160651600-160653800	Genic enhancers	GM12878-XiMat	blood
13	chr1:160651600-160655400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:160651600-160655400	Genic enhancers	Dnd41	blood
15	chr1:160651600-160656400	Genic enhancers	Primary T cells from cord blood	blood
16	chr1:160651600-160656600	Genic enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:160651800-160654200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:160651800-160654800	Strong transcription	Thymus	Thymus
19	chr1:160652200-160654200	Enhancers	Small Intestine	intestine
20	chr1:160652600-160653600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:160652600-160653800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:160652600-160654000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
23	chr1:160652600-160655000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
24	chr1:160652600-160655400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:160652600-160656000	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr1:160652800-160653600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:160652800-160654000	Enhancers	Primary hematopoietic stem cells	blood
28	chr1:160653000-160653600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:160653000-160654200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:160653200-160653800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:160653200-160653800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
32	chr1:160653200-160653800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:160653200-160653800	Weak transcription	Spleen	Spleen
34	chr1:160653200-160654200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr1:160653200-160654400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr1:160653400-160653600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:160653400-160654000	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr1:160653400-160654400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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