Variant report

Variant	rs17398979
Chromosome Location	chr1:86125806-86125807
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	chr1:86046915..86048660-chr1:86125105..86127128,2	K562	blood:
2	chr1:86125056..86127073-chr1:86141967..86144590,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL24A1-1	chr1:86124367-86126130	ENSG00000249070

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10493775	0.87[EUR][1000 genomes]
rs17128149	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17394404	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17396994	0.86[AFR][1000 genomes]
rs17398930	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17399027	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17399721	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17399929	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1775993	0.81[CEU][hapmap]
rs41289767	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs56204143	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs821378	0.81[CEU][hapmap]
rs821390	0.81[CEU][hapmap]
rs821404	0.82[CEU][hapmap]
rs9324152	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
3	chr1:86103600-86141200	Weak transcription	Thymus	Thymus
4	chr1:86103600-86142200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:86103600-86145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:86103600-86145600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:86103600-86157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:86103600-86172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:86103600-86172600	Weak transcription	Gastric	stomach
10	chr1:86106000-86141200	Weak transcription	Lung	lung
11	chr1:86114000-86141200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:86114000-86143600	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:86114400-86142200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:86114400-86163200	Weak transcription	Esophagus	oesophagus
15	chr1:86115200-86146800	Weak transcription	Psoas Muscle	Psoas
16	chr1:86115200-86167600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:86115400-86141000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:86116400-86127000	Weak transcription	Fetal Kidney	kidney
19	chr1:86116400-86143600	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:86116400-86146200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:86116600-86129200	Weak transcription	Aorta	Aorta
22	chr1:86116600-86142200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:86116600-86145400	Weak transcription	Fetal Stomach	stomach
24	chr1:86117000-86165800	Weak transcription	Fetal Brain Female	brain
25	chr1:86117600-86172000	Weak transcription	Small Intestine	intestine
26	chr1:86119200-86133000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:86119200-86142200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:86119200-86142200	Weak transcription	Placenta	Placenta
29	chr1:86119400-86128800	Weak transcription	Fetal Intestine Small	intestine
30	chr1:86119400-86134000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:86119400-86135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:86119400-86140600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:86119400-86140800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:86119400-86142200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:86119400-86142200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:86119400-86143400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:86119600-86138800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:86119600-86140600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:86119600-86142200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:86119600-86157800	Weak transcription	Hela-S3	cervix
41	chr1:86119600-86172000	Weak transcription	Colonic Mucosa	Colon
42	chr1:86119800-86129200	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:86119800-86134000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:86119800-86139600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:86119800-86171800	Weak transcription	Fetal Brain Male	brain
46	chr1:86120000-86129600	Weak transcription	Fetal Intestine Large	intestine
47	chr1:86120000-86134600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:86120000-86135200	Weak transcription	Ovary	ovary
49	chr1:86120000-86135800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:86120000-86136200	Weak transcription	Adipose Nuclei	Adipose

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