Variant report

Variant	rs485338
Chromosome Location	chr1:165875943-165875944
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	chr1:165795932..165799590-chr1:165874555..165878246,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143179	Chromatin interaction
ENSG00000143183	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10800165	0.81[EUR][1000 genomes]
rs12080800	0.85[TSI][hapmap]
rs12125493	0.85[TSI][hapmap]
rs3762365	0.84[CEU][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3790659	0.88[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3806333	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs492467	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs495529	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs506813	0.83[CHD][hapmap]
rs536109	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs544617	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7519919	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7543127	0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs485338	USP21	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165854600-165883000	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:165856600-165878800	Weak transcription	Small Intestine	intestine
3	chr1:165858200-165881200	Strong transcription	Dnd41	blood
4	chr1:165858400-165881000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:165858600-165902400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:165859000-165881000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:165859200-165878000	Strong transcription	Hela-S3	cervix
8	chr1:165859200-165880400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:165859200-165881000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:165859400-165880200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:165859400-165880400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:165859400-165880600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:165859400-165880600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:165859600-165880600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:165860000-165880200	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr1:165867200-165876800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:165867800-165876600	Weak transcription	Psoas Muscle	Psoas
18	chr1:165868400-165880200	Strong transcription	A549	lung
19	chr1:165870200-165882800	Weak transcription	Fetal Brain Male	brain
20	chr1:165870400-165876600	Weak transcription	Spleen	Spleen
21	chr1:165870400-165879400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:165870800-165880800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:165871000-165876000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:165871000-165883200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:165871800-165877000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:165871800-165880000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:165871800-165880800	Strong transcription	Fetal Stomach	stomach
28	chr1:165871800-165882200	Strong transcription	Fetal Brain Female	brain
29	chr1:165872000-165877200	Genic enhancers	HepG2	liver
30	chr1:165872000-165879000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr1:165872000-165879200	Strong transcription	Fetal Intestine Small	intestine
32	chr1:165872000-165879600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:165872000-165879800	Strong transcription	K562	blood
34	chr1:165872200-165876600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:165872200-165879200	Strong transcription	Fetal Intestine Large	intestine
36	chr1:165872400-165883200	Weak transcription	Brain Anterior Caudate	brain
37	chr1:165872400-165883200	Weak transcription	Brain Substantia Nigra	brain
38	chr1:165872800-165876600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:165872800-165883400	Weak transcription	Fetal Kidney	kidney
40	chr1:165873000-165876600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:165873000-165876600	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:165873000-165876600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:165873000-165880000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:165873200-165876400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:165873200-165876400	Weak transcription	Lung	lung
46	chr1:165873200-165876400	Weak transcription	Right Ventricle	heart
47	chr1:165873200-165877800	Weak transcription	Aorta	Aorta
48	chr1:165873200-165879600	Strong transcription	Placenta	Placenta
49	chr1:165873200-165881000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:165873400-165876600	Weak transcription	Brain Inferior Temporal Lobe	brain

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