Variant report

Variant	rs7868270
Chromosome Location	chr9:98648085-98648086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98643243..98646230-chr9:98646548..98650436,4	MCF-7	breast:
2	chr9:98642876..98646721-chr9:98647995..98651810,4	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10759883	0.92[YRI][hapmap]
rs10983321	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10988581	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10988804	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11787559	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11790370	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11790491	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11793298	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11794054	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12001	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12683310	0.83[EUR][1000 genomes]
rs12683634	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12685221	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12685807	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12686222	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12686457	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1360064	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16910262	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16910296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16910298	1.00[CEU][hapmap];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]
rs16910418	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1831228	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1999023	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026032	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2069053	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274653	0.81[EUR][1000 genomes]
rs2274654	0.81[EUR][1000 genomes]
rs34533243	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3780574	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3802438	0.81[EUR][1000 genomes]
rs4532708	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742775	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742781	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743391	0.83[EUR][1000 genomes]
rs4743400	0.81[EUR][1000 genomes]
rs4743417	0.81[EUR][1000 genomes]
rs4743418	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743436	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743472	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7048414	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73536517	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73656544	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[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	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7868270	LINC00476	cis	Esophagus Mucosa	GTEx
rs7868270	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs7868270	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs7868270	LINC00476	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98648400	Weak transcription	Lung	lung
2	chr9:98638800-98649000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:98638800-98654800	Weak transcription	Esophagus	oesophagus
4	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
5	chr9:98639400-98649000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:98639400-98650800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:98639400-98677800	Weak transcription	Placenta	Placenta
8	chr9:98639400-98678000	Weak transcription	Ovary	ovary
9	chr9:98639600-98649200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:98639600-98678000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:98639800-98664200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr9:98639800-98677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:98640000-98649000	Weak transcription	Spleen	Spleen
14	chr9:98640000-98661600	Weak transcription	Right Atrium	heart
15	chr9:98640000-98663600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:98640000-98678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:98640000-98680600	Weak transcription	Colonic Mucosa	Colon
18	chr9:98640000-98685600	Weak transcription	Right Ventricle	heart
19	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr9:98640200-98678200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:98640400-98649200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:98640400-98664800	Weak transcription	Brain Substantia Nigra	brain
23	chr9:98640400-98677800	Weak transcription	Psoas Muscle	Psoas
24	chr9:98640600-98649000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:98640600-98678000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:98641600-98650000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr9:98642200-98652400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:98642200-98654600	Weak transcription	Fetal Intestine Small	intestine
29	chr9:98642200-98663600	Weak transcription	Hela-S3	cervix
30	chr9:98642600-98678000	Weak transcription	Colon Smooth Muscle	Colon
31	chr9:98642600-98680600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:98642800-98668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:98642800-98681800	Weak transcription	Fetal Kidney	kidney
34	chr9:98643000-98648400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:98643200-98648200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr9:98643200-98648400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr9:98643200-98649000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:98643200-98649800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:98643200-98651200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:98643400-98648400	Strong transcription	A549	lung
41	chr9:98643400-98649400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr9:98643600-98648200	Strong transcription	HSMM	muscle
43	chr9:98643600-98649400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:98643600-98649800	Strong transcription	Osteobl	bone
45	chr9:98643800-98648400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr9:98643800-98649600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:98644000-98648200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr9:98644200-98648800	Strong transcription	Fetal Muscle Leg	muscle
49	chr9:98644200-98649400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:98644200-98649600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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