Variant report

Variant	rs10993429
Chromosome Location	chr9:97739465-97739466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97738672..97741509-chr9:97745708..97747354,2	K562	blood:
2	chr9:97680726..97683372-chr9:97738780..97741579,2	MCF-7	breast:
3	chr9:97573279..97576289-chr9:97736282..97739747,3	MCF-7	breast:
4	chr9:97733013..97735373-chr9:97738780..97740333,2	MCF-7	breast:
5	chr9:97685017..97689714-chr9:97737820..97743340,6	MCF-7	breast:
6	chr9:97739328..97741298-chr9:97743641..97746180,2	K562	blood:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10512250	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993358	1.00[GIH][hapmap]
rs10993359	0.86[GIH][hapmap]
rs10993371	1.00[GIH][hapmap]
rs10993409	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993412	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993422	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993423	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993424	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993425	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993426	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993428	1.00[CHB][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993430	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993431	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993438	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993440	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993445	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993446	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993447	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993448	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993450	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236203	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236825	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12238576	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16911884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16911886	0.90[CHB][hapmap]
rs16911887	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802457	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802458	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56855628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57054200	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58325577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59246309	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59630616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7023719	0.85[JPT][hapmap]
rs7848018	0.90[CHB][hapmap];1.00[TSI][hapmap]
rs7857726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866661	0.90[CHB][hapmap];1.00[TSI][hapmap]
rs7867908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875287	0.86[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875888	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10993429	SCGB2A2	trans	brain	seeQTL
rs10993429	C2CD4B	trans	brain	seeQTL
rs10993429	SCGB1D2	trans	brain	seeQTL

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	chr9:97715400-97741200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr9:97715400-97749600	Weak transcription	Thymus	Thymus
7	chr9:97715600-97742000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr9:97715600-97742000	Weak transcription	Psoas Muscle	Psoas
9	chr9:97715600-97742400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:97716000-97742400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:97718800-97744000	Weak transcription	GM12878-XiMat	blood
12	chr9:97719000-97743400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:97719000-97745800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:97719400-97739800	Weak transcription	Primary T cells from cord blood	blood
15	chr9:97719400-97746200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:97719400-97747000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr9:97719600-97747000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:97720800-97741600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:97724800-97743000	Weak transcription	Brain Angular Gyrus	brain
20	chr9:97724800-97743000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:97726800-97742400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:97728000-97742800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr9:97728000-97754200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr9:97728200-97741400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr9:97731600-97743000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:97732600-97739800	Enhancers	Fetal Intestine Large	intestine
27	chr9:97732800-97742400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:97733400-97757600	Weak transcription	Esophagus	oesophagus
29	chr9:97734400-97739800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:97734400-97741200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:97734600-97741400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:97734600-97757600	Weak transcription	Gastric	stomach
33	chr9:97734800-97742400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:97734800-97743000	Weak transcription	Brain Substantia Nigra	brain
35	chr9:97734800-97747200	Weak transcription	Right Atrium	heart
36	chr9:97735000-97742800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr9:97735600-97743000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:97736000-97741400	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:97736000-97742000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr9:97736000-97742200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:97736200-97742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:97736200-97742200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:97736200-97743000	Weak transcription	Brain Anterior Caudate	brain
44	chr9:97736200-97748000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:97736400-97741400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:97736600-97741800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:97736600-97747000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr9:97736600-97757200	Weak transcription	NH-A	brain
49	chr9:97736600-97757400	Weak transcription	NHLF	lung
50	chr9:97736600-97757600	Weak transcription	Adipose Nuclei	Adipose

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