Variant report

Variant	rs1888220
Chromosome Location	chr9:117847613-117847614
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:117839179..117841856-chr9:117845552..117848001,2	MCF-7	breast:
2	chr9:117841964..117843849-chr9:117846217..117848854,2	MCF-7	breast:
3	chr9:117840344..117843174-chr9:117844856..117847663,3	K562	blood:
4	chr9:117843493..117846362-chr9:117847187..117851097,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1061494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250023	0.80[JPT][hapmap]
rs1271449	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1272041	0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1330360	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1360291	0.80[JPT][hapmap]
rs1617917	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1755637	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755641	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757100	0.81[JPT][hapmap]
rs1757108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757109	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1757110	1.00[ASN][1000 genomes]
rs1757111	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482078	0.80[JPT][hapmap]
rs2988578	0.81[JPT][hapmap]
rs2989519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2992147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
3	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117817800-117850600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:117819800-117848000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:117822400-117854400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:117825400-117848000	Weak transcription	Lung	lung
8	chr9:117826800-117849400	Strong transcription	Osteobl	bone
9	chr9:117827000-117848600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:117827000-117849200	Strong transcription	NHDF-Ad	bronchial
11	chr9:117827200-117855200	Strong transcription	NH-A	brain
12	chr9:117827400-117849200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:117831800-117848000	Strong transcription	Stomach Smooth Muscle	stomach
14	chr9:117834000-117849400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:117834000-117849800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:117834800-117848600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:117836000-117848600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:117837000-117849400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:117839000-117848800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:117839000-117849200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr9:117839600-117849200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:117840600-117848000	Weak transcription	Fetal Intestine Large	intestine
23	chr9:117840800-117848600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:117841200-117860600	Weak transcription	Fetal Kidney	kidney
25	chr9:117841400-117849200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:117842600-117850400	Weak transcription	Fetal Brain Female	brain
27	chr9:117842800-117849400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:117842800-117855200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:117843600-117849000	Strong transcription	Fetal Muscle Leg	muscle
30	chr9:117843600-117849400	Strong transcription	NHLF	lung
31	chr9:117845200-117848200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr9:117845600-117848600	Weak transcription	Fetal Lung	lung
33	chr9:117845600-117849000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr9:117845600-117850000	Weak transcription	Gastric	stomach
35	chr9:117845800-117847800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr9:117845800-117849600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:117845800-117850400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:117846200-117849600	Strong transcription	Fetal Stomach	stomach
39	chr9:117846200-117849800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:117846200-117849800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:117846400-117848000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:117846400-117848800	Strong transcription	Aorta	Aorta
43	chr9:117846600-117848000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:117846600-117849600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr9:117846600-117849600	Genic enhancers	NHEK	skin
46	chr9:117846600-117851000	Weak transcription	Right Atrium	heart
47	chr9:117846800-117848400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr9:117846800-117849600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:117847000-117848600	Genic enhancers	Colon Smooth Muscle	Colon
50	chr9:117847000-117849000	Weak transcription	Fetal Muscle Trunk	muscle

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