Variant report

Variant	rs6788864
Chromosome Location	chr3:101289589-101289590
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:6)
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	chr3:101289384-101290430	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:101289433-101289899	K562	blood:	n/a	n/a
3	POLR2A	chr3:101287944-101290521	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:101230224..101236227-chr3:101287209..101294479,8	K562	blood:
2	chr3:101289369..101294999-chr3:101391357..101396813,8	K562	blood:
3	chr3:101289588..101293101-chr3:101394155..101396875,5	MCF-7	breast:
4	chr3:101230038..101233245-chr3:101289410..101293829,6	MCF-7	breast:
5	chr3:101273703..101276448-chr3:101288119..101291518,3	K562	blood:
6	chr3:101288583..101290158-chr3:101290409..101292112,2	K562	blood:

No data

Variant related genes	Relation type
PCNP	TF binding region
ENSG00000256628	Chromatin interaction
ENSG00000138468	Chromatin interaction
ENSG00000066422	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1078153	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11924203	0.89[EUR][1000 genomes]
rs11929578	1.00[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs12491044	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12696325	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13072446	0.87[EUR][1000 genomes]
rs1426386	0.96[EUR][1000 genomes]
rs1464361	0.89[EUR][1000 genomes]
rs1569071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433032	0.86[EUR][1000 genomes]
rs2449824	0.89[EUR][1000 genomes]
rs2460721	0.89[EUR][1000 genomes]
rs2553414	0.89[EUR][1000 genomes]
rs2553420	0.89[EUR][1000 genomes]
rs2553422	0.89[EUR][1000 genomes]
rs2553423	0.89[EUR][1000 genomes]
rs2553428	0.88[EUR][1000 genomes]
rs2611836	0.86[TSI][hapmap]
rs2682387	0.89[EUR][1000 genomes]
rs2682389	0.86[EUR][1000 genomes]
rs3846092	0.89[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs41273611	0.89[EUR][1000 genomes]
rs4234491	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683930	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61379928	0.89[EUR][1000 genomes]
rs6763679	0.89[EUR][1000 genomes]
rs6764700	0.88[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs6768114	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6768182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6779278	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6779775	0.96[EUR][1000 genomes]
rs6791803	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs6794860	0.88[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs6805496	0.86[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs6806256	0.88[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs6809436	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs72942230	0.89[EUR][1000 genomes]
rs72942264	0.89[EUR][1000 genomes]
rs72948053	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7611497	1.00[MEX][hapmap]
rs7613194	0.87[EUR][1000 genomes]
rs7618600	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs7621062	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638284	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7644519	0.89[EUR][1000 genomes]
rs7645698	0.86[EUR][1000 genomes]
rs7648141	0.88[EUR][1000 genomes]
rs9820611	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9917699	0.89[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6788864	FAM55C	cis	brain	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101281400-101292600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:101281800-101292000	Weak transcription	Colonic Mucosa	Colon
3	chr3:101281800-101292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:101281800-101292200	Weak transcription	Esophagus	oesophagus
5	chr3:101281800-101292200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:101282000-101291800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:101282000-101291800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:101282000-101292200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:101282000-101292200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:101282000-101292200	Weak transcription	Right Atrium	heart
11	chr3:101282200-101291600	Weak transcription	Fetal Lung	lung
12	chr3:101282200-101292200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:101282200-101292600	Weak transcription	Aorta	Aorta
14	chr3:101282400-101289800	Weak transcription	Psoas Muscle	Psoas
15	chr3:101282400-101291800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:101282400-101292000	Weak transcription	Right Ventricle	heart
17	chr3:101282400-101292200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:101282400-101292400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:101282400-101292600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:101282400-101292600	Weak transcription	Spleen	Spleen
21	chr3:101282600-101292000	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:101282600-101292200	Weak transcription	Small Intestine	intestine
23	chr3:101282800-101289600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:101282800-101291400	Weak transcription	Fetal Heart	heart
25	chr3:101283000-101292600	Weak transcription	Gastric	stomach
26	chr3:101285000-101289600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:101285000-101291600	Weak transcription	Fetal Kidney	kidney
28	chr3:101285000-101291800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:101285000-101291800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:101285000-101292400	Weak transcription	Ovary	ovary
31	chr3:101285200-101291800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:101285200-101292000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:101285200-101292000	Weak transcription	Fetal Brain Male	brain
34	chr3:101285400-101290200	Weak transcription	Hela-S3	cervix
35	chr3:101285400-101291600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:101285400-101291600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:101285400-101292000	Weak transcription	Brain Angular Gyrus	brain
38	chr3:101285400-101292000	Weak transcription	Brain Anterior Caudate	brain
39	chr3:101285400-101292000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:101285600-101289600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:101285600-101290200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:101285600-101291600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:101285600-101291800	Weak transcription	HSMMtube	muscle
44	chr3:101285600-101292000	Weak transcription	Liver	Liver
45	chr3:101285600-101292000	Weak transcription	Osteobl	bone
46	chr3:101285600-101292200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:101285600-101292200	Weak transcription	Placenta	Placenta
48	chr3:101285600-101292200	Weak transcription	Left Ventricle	heart
49	chr3:101285600-101292600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:101285800-101291800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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