Variant report

Variant	rs7038998
Chromosome Location	chr9:100662396-100662397
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100662130..100664191-chr9:100669480..100671871,2	MCF-7	breast:
2	chr9:100661983..100664921-chr9:100679667..100682904,3	MCF-7	breast:
3	chr9:100459617..100461117-chr9:100662395..100665046,2	K562	blood:
4	chr9:100659963..100662557-chr9:100683165..100684885,2	MCF-7	breast:
5	chr9:100472331..100474659-chr9:100661495..100663570,2	MCF-7	breast:
6	chr9:100661987..100664493-chr9:100807895..100810404,2	K562	blood:

Variant related genes	Relation type
ENSG00000136936	Chromatin interaction
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10113884	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10115216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117642	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10119760	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119853	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10120412	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10122541	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123699	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10512255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512256	1.00[YRI][hapmap]
rs1059003	1.00[YRI][hapmap]
rs10739526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs10759975	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10759981	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10760011	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs10818175	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10818213	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10818241	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10984079	0.83[ASN][1000 genomes]
rs10984103	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10984134	0.83[ASN][1000 genomes]
rs10984156	0.83[ASN][1000 genomes]
rs10984195	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs10984218	0.87[ASN][1000 genomes]
rs10984222	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs10984230	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10984235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10984253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984311	0.86[CHB][hapmap]
rs10984377	1.00[YRI][hapmap]
rs10984424	0.82[CHB][hapmap]
rs10984516	1.00[YRI][hapmap]
rs10984532	1.00[YRI][hapmap]
rs10984545	1.00[YRI][hapmap]
rs12004762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12006522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342417	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12343182	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12347191	0.81[EUR][1000 genomes]
rs12375612	1.00[YRI][hapmap]
rs12550872	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13286291	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13287360	0.92[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13299924	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1348387	1.00[YRI][hapmap]
rs1443434	0.92[CEU][hapmap]
rs1443435	0.92[CEU][hapmap]
rs1443436	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1561957	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561961	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17687621	1.00[YRI][hapmap]
rs1867278	0.83[CEU][hapmap]
rs1947015	1.00[YRI][hapmap]
rs1955143	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1955144	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1955145	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2120262	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2120264	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282190	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs2417575	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2417576	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28417086	0.87[ASN][1000 genomes]
rs28697997	0.87[ASN][1000 genomes]
rs28703314	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3021525	0.85[ASN][1000 genomes]
rs35324451	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3758249	0.92[CEU][hapmap]
rs3758250	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs3758251	0.92[CEU][hapmap]
rs3808893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808895	0.89[CHB][hapmap]
rs3824495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4255258	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4460498	0.81[EUR][1000 genomes]
rs4743139	0.92[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4743142	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6478445	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6478469	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478471	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027221	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][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]
rs7031386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032086	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7032114	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034249	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7034648	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037175	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7037324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044121	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7044799	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048255	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753537	0.91[ASN][1000 genomes]
rs7851498	1.00[YRI][hapmap]
rs7854948	1.00[YRI][hapmap]
rs7860144	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7866436	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868534	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs894673	0.92[CEU][hapmap]
rs907577	0.92[CEU][hapmap]
rs907581	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs925487	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9299258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9775370	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs993501	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7038998	C9orf156	cis	Frontal Cortex	GTEx
rs7038998	C9orf156	cis	Temporal Cortex	GTEx
rs7038998	Hs.43687	cis	multi-tissue	Pritchard

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100652600-100662400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr9:100652800-100666600	Weak transcription	Fetal Lung	lung
3	chr9:100653000-100662600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:100653000-100663400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr9:100653000-100667000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:100654200-100666600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:100654600-100662400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:100656000-100662400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:100656000-100662400	Weak transcription	Primary B cells from cord blood	blood
10	chr9:100656000-100662400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:100656000-100662400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr9:100656000-100662600	Weak transcription	Adipose Nuclei	Adipose
13	chr9:100656000-100667600	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:100656000-100669400	Weak transcription	Brain Substantia Nigra	brain
15	chr9:100656200-100662800	Weak transcription	HSMM	muscle
16	chr9:100656200-100665600	Weak transcription	Dnd41	blood
17	chr9:100656200-100666800	Weak transcription	Brain Germinal Matrix	brain
18	chr9:100656200-100670400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:100656400-100668400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:100656400-100669800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:100656400-100669800	Weak transcription	Fetal Brain Female	brain
22	chr9:100656600-100663000	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:100656600-100667000	Weak transcription	Brain Anterior Caudate	brain
24	chr9:100656800-100666800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:100656800-100668400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:100656800-100669400	Weak transcription	Left Ventricle	heart
27	chr9:100656800-100672400	Weak transcription	Stomach Mucosa	stomach
28	chr9:100657000-100662600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr9:100657000-100666600	Weak transcription	Placenta	Placenta
30	chr9:100657000-100669400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:100657000-100669400	Weak transcription	Right Ventricle	heart
32	chr9:100658000-100665000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr9:100658200-100664800	Weak transcription	Fetal Intestine Large	intestine
34	chr9:100658200-100671600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr9:100658400-100662400	Weak transcription	Fetal Thymus	thymus
36	chr9:100658400-100662600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:100658400-100669400	Weak transcription	Hela-S3	cervix
38	chr9:100658400-100671600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:100658600-100662400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:100658600-100662400	Weak transcription	Spleen	Spleen
41	chr9:100658600-100662600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:100658600-100662600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:100658600-100662600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr9:100658600-100662800	Weak transcription	A549	lung
45	chr9:100658600-100662800	Weak transcription	NHEK	skin
46	chr9:100658600-100663000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:100658600-100665200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:100658600-100666600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:100658600-100666800	Weak transcription	Pancreas	Pancrea
50	chr9:100658600-100667600	Weak transcription	Brain Inferior Temporal Lobe	brain

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