Variant report

Variant	rs1004427
Chromosome Location	chr9:97742111-97742112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97740546..97743135-chr9:97764674..97767622,2	K562	blood:
2	chr9:97741635..97744525-chr9:97765545..97768244,3	K562	blood:
3	chr9:97685017..97689714-chr9:97737820..97743340,6	MCF-7	breast:
4	chr9:97741056..97743749-chr9:97766661..97768613,2	MCF-7	breast:
5	chr9:97688920..97691846-chr9:97741162..97743776,2	K562	blood:
6	chr9:97740253..97742678-chr9:97742723..97744837,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1004813	1.00[CEU][hapmap]
rs10512250	0.90[CHB][hapmap]
rs10512252	1.00[CEU][hapmap]
rs10993409	0.91[CHB][hapmap]
rs10993410	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993420	0.91[CHB][hapmap]
rs10993422	0.90[CHB][hapmap]
rs10993423	0.90[CHB][hapmap]
rs10993425	0.91[CHB][hapmap]
rs10993428	0.85[CHB][hapmap]
rs10993429	0.90[CHB][hapmap]
rs10993435	0.91[JPT][hapmap]
rs10993441	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10993443	0.91[CHB][hapmap]
rs10993445	0.91[CHB][hapmap]
rs10993446	0.90[CHB][hapmap]
rs10993448	0.86[CHB][hapmap]
rs10993449	0.91[JPT][hapmap]
rs10993451	0.89[CHB][hapmap]
rs12236420	0.91[CHB][hapmap]
rs12236825	0.91[CHB][hapmap]
rs12238576	0.91[CHB][hapmap]
rs12682668	1.00[CEU][hapmap]
rs12684139	1.00[CEU][hapmap]
rs12684461	1.00[CEU][hapmap]
rs12684470	1.00[CEU][hapmap]
rs12686277	1.00[CEU][hapmap]
rs12686500	1.00[CEU][hapmap]
rs16905557	1.00[CEU][hapmap]
rs16911801	1.00[CEU][hapmap]
rs16911802	1.00[CEU][hapmap]
rs16911817	1.00[CEU][hapmap]
rs16911821	1.00[CEU][hapmap]
rs16911826	1.00[CEU][hapmap]
rs16911884	0.91[CHB][hapmap]
rs16911886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16911887	0.90[CHB][hapmap]
rs2078379	1.00[CEU][hapmap]
rs28495509	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896816	0.91[JPT][hapmap]
rs3802457	0.90[CHB][hapmap]
rs3802458	0.90[CHB][hapmap]
rs3847309	1.00[CEU][hapmap]
rs3847310	1.00[CEU][hapmap]
rs3886567	1.00[CEU][hapmap]
rs55814604	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042271	0.90[JPT][hapmap]
rs72750344	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750350	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750352	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750370	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7465900	1.00[CEU][hapmap]
rs7848018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867908	0.91[CHB][hapmap]
rs7875888	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	esv1655411	chr9:97742111-97742112	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97713800-97757400	Weak transcription	Fetal Brain Female	brain
3	chr9:97715000-97758200	Weak transcription	Spleen	Spleen
4	chr9:97715200-97748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:97715400-97749600	Weak transcription	Thymus	Thymus
6	chr9:97715600-97742400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:97716000-97742400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:97718800-97744000	Weak transcription	GM12878-XiMat	blood
9	chr9:97719000-97743400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:97719000-97745800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:97719400-97746200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:97719400-97747000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:97719600-97747000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:97724800-97743000	Weak transcription	Brain Angular Gyrus	brain
15	chr9:97724800-97743000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:97726800-97742400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:97728000-97742800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:97728000-97754200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:97731600-97743000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:97732800-97742400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:97733400-97757600	Weak transcription	Esophagus	oesophagus
22	chr9:97734600-97757600	Weak transcription	Gastric	stomach
23	chr9:97734800-97742400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:97734800-97743000	Weak transcription	Brain Substantia Nigra	brain
25	chr9:97734800-97747200	Weak transcription	Right Atrium	heart
26	chr9:97735000-97742800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr9:97735600-97743000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:97736000-97742200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:97736200-97742200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:97736200-97743000	Weak transcription	Brain Anterior Caudate	brain
31	chr9:97736200-97748000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:97736600-97747000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr9:97736600-97757200	Weak transcription	NH-A	brain
34	chr9:97736600-97757400	Weak transcription	NHLF	lung
35	chr9:97736600-97757600	Weak transcription	Adipose Nuclei	Adipose
36	chr9:97736600-97757600	Weak transcription	Osteobl	bone
37	chr9:97736600-97766200	Weak transcription	Right Ventricle	heart
38	chr9:97737000-97742200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:97737000-97757200	Weak transcription	Fetal Heart	heart
40	chr9:97737000-97758200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:97738000-97747200	Weak transcription	Pancreas	Pancrea
42	chr9:97738000-97757600	Weak transcription	Lung	lung
43	chr9:97738200-97757600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:97738400-97742400	Weak transcription	Aorta	Aorta
45	chr9:97738600-97742400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr9:97738600-97745200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:97738600-97745600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr9:97738600-97749200	Weak transcription	Ovary	ovary
49	chr9:97738600-97753600	Weak transcription	Fetal Lung	lung
50	chr9:97738600-97757200	Weak transcription	Muscle Satellite Cultured Cells	--

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