Variant report

Variant	rs6005671
Chromosome Location	chr22:28321217-28321218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:28320791-28322398	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114236180..114238815-chr22:28319168..28321227,2	MCF-7	breast:
2	chr22:28314240..28318483-chr22:28320569..28325658,5	MCF-7	breast:
3	chr22:28317023..28318646-chr22:28319576..28321605,2	MCF-7	breast:
4	chr22:28315358..28317239-chr22:28319589..28322630,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSCB-1	chr22:28318007-28321384	NONHSAT084606

No data

Variant related genes	Relation type
MIR3199-2	TF binding region
ENSG00000235954	Chromatin interaction
ENSG00000180957	Chromatin interaction
ENSG00000264073	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs118839	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs138631	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs138638	0.89[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs138650	0.89[CEU][hapmap];0.83[CHD][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs138685	0.81[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap]
rs1548235	0.83[CHD][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap]
rs2038158	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2267121	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs2267124	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3747141	0.83[CHD][hapmap]
rs4140571	0.89[CEU][hapmap];0.88[CHD][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs470100	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs470105	0.81[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs5752667	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762393	0.89[ASN][1000 genomes]
rs5762416	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762418	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997319	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs720621	0.89[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73425788	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs738451	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs957601	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6005671	ZNF280A	cis	cerebellum	SCAN
rs6005671	MED30	trans	cerebellum	SCAN
rs6005671	TTC28AS	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28316200-28326200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:28316200-28328400	Weak transcription	Aorta	Aorta
3	chr22:28316200-28337400	Weak transcription	Ovary	ovary
4	chr22:28316400-28321400	Weak transcription	Spleen	Spleen
5	chr22:28316400-28322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr22:28316400-28322400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr22:28316400-28322600	Weak transcription	HSMMtube	muscle
8	chr22:28316400-28326400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr22:28316400-28326400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr22:28316400-28326400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr22:28316400-28326400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr22:28316400-28326600	Weak transcription	Right Ventricle	heart
13	chr22:28316400-28327000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr22:28316400-28328200	Weak transcription	Left Ventricle	heart
15	chr22:28316400-28329000	Weak transcription	Pancreas	Pancrea
16	chr22:28316400-28329000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr22:28316400-28335000	Weak transcription	Colonic Mucosa	Colon
18	chr22:28316400-28336800	Weak transcription	Fetal Muscle Leg	muscle
19	chr22:28316400-28342600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr22:28316400-28358600	Weak transcription	Placenta	Placenta
21	chr22:28316400-28370200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr22:28316400-28376800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr22:28316400-28378000	Weak transcription	Esophagus	oesophagus
24	chr22:28316600-28323200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr22:28316600-28325400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr22:28316600-28328600	Weak transcription	Stomach Mucosa	stomach
27	chr22:28316600-28348400	Weak transcription	Brain Substantia Nigra	brain
28	chr22:28316800-28322400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr22:28316800-28325400	Weak transcription	Psoas Muscle	Psoas
30	chr22:28316800-28325800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr22:28316800-28326600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr22:28316800-28329000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr22:28316800-28333800	Weak transcription	Brain Hippocampus Middle	brain
34	chr22:28316800-28336600	Weak transcription	Fetal Intestine Large	intestine
35	chr22:28316800-28340400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr22:28317000-28322000	Weak transcription	NH-A	brain
37	chr22:28317000-28322800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr22:28317000-28323800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr22:28317000-28325400	Weak transcription	HMEC	breast
40	chr22:28317000-28325800	Weak transcription	NHEK	skin
41	chr22:28317000-28326000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr22:28317000-28327400	Weak transcription	Adipose Nuclei	Adipose
43	chr22:28317000-28338800	Weak transcription	Fetal Intestine Small	intestine
44	chr22:28317000-28340800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr22:28317000-28348200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr22:28317200-28322000	Weak transcription	Colon Smooth Muscle	Colon
47	chr22:28317200-28323200	Weak transcription	Brain Anterior Caudate	brain
48	chr22:28317200-28336600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr22:28317400-28321400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr22:28317400-28325000	Weak transcription	HSMM	muscle

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