Variant report

Variant	rs6797630
Chromosome Location	chr3:113308922-113308923
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA2018-1	chr3:113308630-113309036	ENSG00000239453.1

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13327031	0.81[EUR][1000 genomes]
rs13353449	0.81[EUR][1000 genomes]
rs2399487	0.81[EUR][1000 genomes]
rs28539944	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28614095	1.00[EUR][1000 genomes]
rs4419353	0.81[EUR][1000 genomes]
rs6438154	0.81[EUR][1000 genomes]
rs6779241	0.81[EUR][1000 genomes]
rs6780720	0.81[EUR][1000 genomes]
rs6781507	0.81[EUR][1000 genomes]
rs6808103	0.81[EUR][1000 genomes]
rs72950893	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72950895	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645188	0.81[EUR][1000 genomes]
rs9810754	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9827490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9827772	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9829540	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9846529	1.00[EUR][1000 genomes]
rs9860473	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9878186	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh 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	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113280200-113321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:113280600-113314800	Weak transcription	Spleen	Spleen
3	chr3:113285200-113329800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:113285200-113343400	Weak transcription	Small Intestine	intestine
5	chr3:113286000-113316800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:113294400-113321600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:113296800-113324200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:113297400-113315600	Strong transcription	GM12878-XiMat	blood
9	chr3:113298800-113309400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:113298800-113315200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:113299400-113315400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:113299600-113309400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr3:113302200-113309400	Strong transcription	Primary B cells from cord blood	blood
14	chr3:113304800-113309000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:113304800-113311800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:113305000-113309000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:113305000-113325000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:113305200-113309200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:113305400-113309000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:113305400-113309000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:113305400-113309000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:113305400-113309200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:113305400-113309800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:113305600-113312000	Weak transcription	Gastric	stomach
25	chr3:113305600-113324600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:113305800-113322800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:113306000-113320400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:113306400-113309200	Strong transcription	Primary hematopoietic stem cells	blood
29	chr3:113308000-113309000	Weak transcription	Primary T cells from cord blood	blood
30	chr3:113308000-113309000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:113308000-113320400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:113308200-113309000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:113308200-113311800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:113308200-113311800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:113308200-113311800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:113308400-113320800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:113308400-113321400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:113308800-113309000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:113308800-113309000	Enhancers	Fetal Thymus	thymus
40	chr3:113308800-113309200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:113308800-113310000	Active TSS	Thymus	Thymus
42	chr3:113308800-113310200	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr3:113308800-113310400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr3:113308800-113310400	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr3:113308800-113310400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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