Variant report

Variant	rs7550448
Chromosome Location	chr1:174974939-174974940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:174972571-174978477	K562	blood:	n/a	n/a
2	POLR2A	chr1:174974248-174974984	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:174974139-174975212	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174968308..174972682-chr1:174973669..174977278,7	MCF-7	breast:
2	chr1:174966455..174979047-chr1:174985921..174994239,29	MCF-7	breast:
3	chr1:174868186..174869826-chr1:174973166..174975572,2	K562	blood:
4	chr1:174973206..174975199-chr1:174975855..174978492,3	MCF-7	breast:
5	chr1:174966903..174971287-chr1:174971534..174977740,10	MCF-7	breast:

No data

Variant related genes	Relation type
CACYBP	TF binding region
ENSG00000120333	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000206659	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10912860	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10912867	0.90[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11582831	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12119351	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12122361	1.00[CHB][hapmap]
rs12122399	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12124150	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12125682	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12723394	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12753457	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34484492	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56978149	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59663317	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6691857	1.00[CHB][hapmap]
rs6700816	1.00[CHB][hapmap]
rs7533443	0.81[AFR][1000 genomes]
rs7537508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][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	nsv1001000	chr1:174944208-174978853	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7550448	RC3H1	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174969800-174981600	Weak transcription	Gastric	stomach
2	chr1:174970000-174977000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:174970000-174977200	Weak transcription	Lung	lung
4	chr1:174970000-174977200	Weak transcription	Pancreas	Pancrea
5	chr1:174970000-174982400	Weak transcription	Esophagus	oesophagus
6	chr1:174970000-174991800	Weak transcription	Stomach Mucosa	stomach
7	chr1:174970200-174976600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:174970200-174977000	Weak transcription	Colonic Mucosa	Colon
9	chr1:174970200-174981200	Weak transcription	Right Ventricle	heart
10	chr1:174970400-174976800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:174970400-174977200	Weak transcription	Aorta	Aorta
12	chr1:174970600-174977200	Weak transcription	Fetal Stomach	stomach
13	chr1:174970600-174981800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:174970800-174975800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:174970800-174975800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:174970800-174976800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:174970800-174977200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:174970800-174980800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:174970800-174986000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:174971000-174991600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:174971200-174976400	Weak transcription	Spleen	Spleen
22	chr1:174971200-174976400	Weak transcription	HUVEC	blood vessel
23	chr1:174971200-174977200	Weak transcription	Brain Germinal Matrix	brain
24	chr1:174971600-174977200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:174971800-174977800	Weak transcription	Fetal Heart	heart
26	chr1:174972000-174981000	Weak transcription	Fetal Intestine Small	intestine
27	chr1:174972200-174975800	Weak transcription	Osteobl	bone
28	chr1:174972200-174976400	Weak transcription	NHLF	lung
29	chr1:174972200-174977400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:174972600-174977000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:174972600-174977200	Weak transcription	Ovary	ovary
32	chr1:174972600-174981800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:174972800-174975800	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:174973000-174982200	Weak transcription	Fetal Brain Male	brain
35	chr1:174973000-174990600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:174973200-174976000	Weak transcription	HSMMtube	muscle
37	chr1:174973200-174976200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:174973200-174976400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:174973200-174976400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:174973200-174976400	Weak transcription	Fetal Lung	lung
41	chr1:174973200-174976600	Weak transcription	Psoas Muscle	Psoas
42	chr1:174973200-174978600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:174973200-174982000	Weak transcription	Small Intestine	intestine
44	chr1:174973200-174983600	Strong transcription	K562	blood
45	chr1:174973200-174987800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:174973200-174987800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:174973200-174988200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:174973400-174976400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:174973600-174987800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:174973600-174988200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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