Variant report

Variant	rs2364398
Chromosome Location	chr7:140431694-140431695
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	chr7:140402003..140403554-chr7:140431273..140432954,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090266	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10241711	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10242534	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10247116	0.92[GIH][hapmap];0.94[LWK][hapmap]
rs10269699	0.92[GIH][hapmap];0.94[LWK][hapmap]
rs1046515	0.93[EUR][1000 genomes]
rs12375245	0.92[GIH][hapmap];0.93[EUR][1000 genomes]
rs1267600	0.83[EUR][1000 genomes]
rs1267601	0.92[GIH][hapmap];0.94[LWK][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1267606	0.92[GIH][hapmap];0.82[EUR][1000 genomes]
rs1267609	0.88[EUR][1000 genomes]
rs1267611	0.92[GIH][hapmap];0.88[EUR][1000 genomes]
rs1267613	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1267614	0.92[GIH][hapmap];0.92[EUR][1000 genomes]
rs1267617	0.92[EUR][1000 genomes]
rs1267619	0.92[GIH][hapmap]
rs1267633	0.85[EUR][1000 genomes]
rs1267636	0.92[GIH][hapmap];0.97[LWK][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1267638	0.92[GIH][hapmap];0.97[LWK][hapmap];0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1267639	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1267640	0.92[EUR][1000 genomes]
rs1267642	0.92[GIH][hapmap];0.92[EUR][1000 genomes]
rs1267644	0.92[EUR][1000 genomes]
rs1267649	0.92[GIH][hapmap];0.92[EUR][1000 genomes]
rs1270193	0.92[EUR][1000 genomes]
rs1639675	0.92[EUR][1000 genomes]
rs1639678	0.92[EUR][1000 genomes]
rs1639679	0.92[GIH][hapmap];0.88[EUR][1000 genomes]
rs17161666	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17161668	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17161737	0.85[EUR][1000 genomes]
rs17161750	0.92[GIH][hapmap]
rs1733827	0.92[GIH][hapmap];0.97[LWK][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1733832	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1812162	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2245716	0.92[EUR][1000 genomes]
rs2364396	0.92[GIH][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2535947	0.82[EUR][1000 genomes]
rs2535951	0.92[GIH][hapmap];0.97[LWK][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs28577882	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4725799	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4727021	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4727036	0.93[EUR][1000 genomes]
rs4727040	0.92[GIH][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4727041	0.92[GIH][hapmap];0.93[EUR][1000 genomes]
rs4727053	0.95[EUR][1000 genomes]
rs6464036	0.92[GIH][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6464123	0.92[GIH][hapmap]
rs6464149	0.92[GIH][hapmap];0.89[LWK][hapmap]
rs6464984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6949396	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6962426	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6969779	0.95[EUR][1000 genomes]
rs73489531	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73489562	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73491672	0.93[EUR][1000 genomes]
rs73491871	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7792746	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351231	chr7:140390303-140588539	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv831158	chr7:140392222-140602315	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv869260	chr7:140404835-140542905	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1015269	chr7:140412464-140458821	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2364398	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140398000-140466600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:140398200-140473800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:140398200-140492600	Weak transcription	Colonic Mucosa	Colon
4	chr7:140398400-140432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:140398600-140459400	Weak transcription	Brain Germinal Matrix	brain
6	chr7:140398600-140491800	Weak transcription	Fetal Brain Male	brain
7	chr7:140399400-140468200	Weak transcription	Right Ventricle	heart
8	chr7:140399600-140443800	Weak transcription	Fetal Heart	heart
9	chr7:140400000-140474000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:140404400-140452400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:140404800-140489000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:140404800-140517000	Weak transcription	Psoas Muscle	Psoas
13	chr7:140405200-140470800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:140405600-140472200	Weak transcription	Brain Substantia Nigra	brain
15	chr7:140406600-140472800	Weak transcription	Hela-S3	cervix
16	chr7:140407000-140454200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:140407000-140466800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:140407200-140433600	Weak transcription	Adipose Nuclei	Adipose
19	chr7:140407200-140437600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:140407200-140438000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr7:140407200-140438200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:140407200-140438200	Weak transcription	Ovary	ovary
23	chr7:140407200-140438200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:140407200-140438200	Weak transcription	HepG2	liver
25	chr7:140407200-140438600	Weak transcription	Left Ventricle	heart
26	chr7:140407200-140438800	Weak transcription	Brain Anterior Caudate	brain
27	chr7:140407200-140445400	Weak transcription	Spleen	Spleen
28	chr7:140407200-140449800	Weak transcription	A549	lung
29	chr7:140407200-140450000	Weak transcription	Pancreas	Pancrea
30	chr7:140407200-140454400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:140407200-140459200	Weak transcription	Fetal Lung	lung
32	chr7:140407200-140468400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr7:140415000-140437800	Weak transcription	Fetal Brain Female	brain
34	chr7:140415000-140454200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:140415000-140504400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:140415200-140436600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:140415200-140437600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr7:140415200-140438400	Weak transcription	Thymus	Thymus
39	chr7:140415200-140466400	Weak transcription	Aorta	Aorta
40	chr7:140415200-140472000	Weak transcription	Lung	lung
41	chr7:140415200-140506600	Weak transcription	Gastric	stomach
42	chr7:140415600-140433800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:140415600-140437000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr7:140415800-140436600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:140420000-140443600	Weak transcription	GM12878-XiMat	blood
46	chr7:140420400-140437200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr7:140420800-140437600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:140421400-140432200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr7:140421800-140474000	Weak transcription	Brain Angular Gyrus	brain
50	chr7:140422400-140439400	Weak transcription	Fetal Kidney	kidney

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