Variant report

Variant	rs1220413
Chromosome Location	chr1:9927254-9927255
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:9686799..9687772-chr1:9927194..9928142,9	MCF-7	breast:
2	chr1:9921008..9924998-chr1:9925415..9929659,6	K562	blood:
3	chr1:9919706..9921692-chr1:9924809..9927452,2	MCF-7	breast:
4	chr1:9844361..9845392-chr1:9927251..9928213,4	MCF-7	breast:
5	chr1:9926113..9928520-chr1:9934932..9937483,2	MCF-7	breast:
6	chr1:9781386..9784652-chr1:9924402..9927637,3	K562	blood:
7	chr1:9784825..9785795-chr1:9927202..9928673,4	MCF-7	breast:
8	chr1:9882893..9885671-chr1:9926965..9929372,3	MCF-7	breast:
9	chr1:9686678..9687699-chr1:9926083..9928536,12	K562	blood:
10	chr1:9921625..9924250-chr1:9926048..9928989,2	K562	blood:
11	chr1:9851605..9853089-chr1:9927228..9928149,4	MCF-7	breast:
12	chr1:9844311..9845253-chr1:9926813..9928252,17	K562	blood:
13	chr1:9776177..9777877-chr1:9924874..9927491,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000171608	Chromatin interaction
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1220381	0.82[EUR][1000 genomes]
rs1220382	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220383	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1220384	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1220391	0.89[ASN][1000 genomes]
rs1220392	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1220393	0.88[EUR][1000 genomes]
rs1220394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220396	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1220404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1220405	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1220406	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220409	1.00[ASN][1000 genomes]
rs1220411	0.92[EUR][1000 genomes]
rs1220412	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1220418	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1372106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1660735	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083577	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2379108	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486084	0.87[EUR][1000 genomes]
rs2582980	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582981	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3120822	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7225	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs935073	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs935074	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935075	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs946275	1.00[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9904000-9929800	Weak transcription	Aorta	Aorta
2	chr1:9904200-9927400	Weak transcription	Colonic Mucosa	Colon
3	chr1:9904200-9927800	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:9904400-9927800	Weak transcription	Stomach Mucosa	stomach
5	chr1:9904400-9930000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:9904600-9935000	Weak transcription	Osteobl	bone
7	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
8	chr1:9906600-9927400	Weak transcription	Liver	Liver
9	chr1:9907000-9930000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:9907400-9929800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:9910000-9935000	Weak transcription	NHLF	lung
12	chr1:9911000-9927400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:9911000-9930400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:9911200-9932400	Weak transcription	Fetal Heart	heart
15	chr1:9912200-9929600	Weak transcription	Primary B cells from cord blood	blood
16	chr1:9912200-9929600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:9913400-9927400	Weak transcription	Fetal Brain Male	brain
18	chr1:9913600-9927800	Weak transcription	Brain Angular Gyrus	brain
19	chr1:9914000-9927400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:9914000-9927400	Weak transcription	Dnd41	blood
21	chr1:9914000-9927800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:9914000-9929600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:9914000-9929800	Weak transcription	Primary T cells from cord blood	blood
24	chr1:9915800-9928400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:9915800-9935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:9917800-9934400	Strong transcription	Fetal Intestine Small	intestine
27	chr1:9918000-9932800	Strong transcription	Fetal Brain Female	brain
28	chr1:9918200-9932800	Strong transcription	Lung	lung
29	chr1:9918600-9943800	Weak transcription	Small Intestine	intestine
30	chr1:9920000-9929400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:9920000-9929400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:9920000-9929600	Weak transcription	Thymus	Thymus
33	chr1:9920000-9930400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:9920200-9927800	Weak transcription	HMEC	breast
35	chr1:9920200-9929600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:9920200-9930400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:9920200-9932200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:9920200-9935200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:9920400-9927600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:9920400-9930000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:9920400-9930400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:9921000-9934800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:9921200-9929600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:9921200-9932600	Weak transcription	HSMMtube	muscle
45	chr1:9921400-9932400	Weak transcription	HSMM	muscle
46	chr1:9921600-9930000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:9921800-9928400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:9921800-9929800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:9921800-9934800	Weak transcription	Right Atrium	heart
50	chr1:9922000-9933200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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