Variant report

Variant	rs987142
Chromosome Location	chr9:100774646-100774647
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100742523..100748760-chr9:100770717..100780283,13	MCF-7	breast:
2	chr9:100749471..100752077-chr9:100773011..100775688,2	MCF-7	breast:
3	chr9:100756765..100758556-chr9:100774591..100777214,2	MCF-7	breast:
4	chr9:100772538..100774989-chr9:100776767..100778776,2	MCF-7	breast:
5	chr9:100688998..100692524-chr9:100770789..100774886,3	K562	blood:
6	chr9:100696013..100699012-chr9:100772945..100774984,2	K562	blood:
7	chr9:100743154..100749212-chr9:100770478..100774741,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136938	Chromatin interaction
ENSG00000236896	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1010777	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10116946	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10125654	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10984606	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1131641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572025	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1815275	0.91[ASN][1000 genomes]
rs4742710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[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];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743154	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56145417	0.98[EUR][1000 genomes]
rs7035650	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7044744	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7855077	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7855088	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7870926	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7874518	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs879275	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs987142	C9orf102	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100752000-100784000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:100754600-100784200	Strong transcription	Dnd41	blood
3	chr9:100754600-100784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:100755200-100782200	Strong transcription	HepG2	liver
5	chr9:100755200-100783800	Strong transcription	NHEK	skin
6	chr9:100755400-100783000	Weak transcription	Stomach Mucosa	stomach
7	chr9:100755600-100784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:100755800-100782200	Strong transcription	K562	blood
9	chr9:100756000-100777800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:100756400-100783600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:100756400-100783800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr9:100756400-100784400	Strong transcription	Fetal Thymus	thymus
13	chr9:100756600-100785600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr9:100756800-100781200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:100756800-100783000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:100756800-100783400	Strong transcription	HMEC	breast
17	chr9:100757000-100781000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr9:100757000-100785200	Strong transcription	Placenta	Placenta
19	chr9:100757200-100783600	Strong transcription	Liver	Liver
20	chr9:100757400-100784000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:100757600-100784400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:100757800-100782200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:100758400-100780800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr9:100760800-100783600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr9:100761800-100784400	Strong transcription	Thymus	Thymus
26	chr9:100762600-100785400	Strong transcription	Primary T cells from cord blood	blood
27	chr9:100763800-100781800	Strong transcription	Hela-S3	cervix
28	chr9:100764000-100775000	Strong transcription	NHDF-Ad	bronchial
29	chr9:100764400-100784200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:100764400-100784200	Strong transcription	GM12878-XiMat	blood
31	chr9:100765000-100781600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:100765400-100775800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:100765600-100783000	Weak transcription	Right Atrium	heart
34	chr9:100765800-100782800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr9:100765800-100784000	Strong transcription	Adipose Nuclei	Adipose
36	chr9:100766000-100779600	Weak transcription	Fetal Brain Male	brain
37	chr9:100766000-100782400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr9:100766400-100783400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:100766600-100775000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
40	chr9:100767000-100778000	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr9:100767000-100784600	Strong transcription	Fetal Stomach	stomach
42	chr9:100767200-100775800	Strong transcription	Esophagus	oesophagus
43	chr9:100767200-100776000	Strong transcription	Colonic Mucosa	Colon
44	chr9:100767200-100776400	Strong transcription	Fetal Kidney	kidney
45	chr9:100767200-100778800	Strong transcription	Fetal Brain Female	brain
46	chr9:100767200-100778800	Strong transcription	Ovary	ovary
47	chr9:100767200-100781400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr9:100767200-100782200	Strong transcription	Fetal Lung	lung
49	chr9:100767200-100782200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr9:100767200-100782400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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