Variant report

Variant	rs56940988
Chromosome Location	chr7:140450216-140450217
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140395873..140397806-chr7:140448733..140451318,2	MCF-7	breast:
2	chr7:140448573..140452334-chr7:140454838..140458113,4	K562	blood:
3	chr7:140429621..140431191-chr7:140448921..140450687,2	K562	blood:
4	chr7:140442723..140444606-chr7:140448955..140450528,2	K562	blood:
5	chr7:140443740..140445240-chr7:140449142..140451877,2	MCF-7	breast:
6	chr7:140449958..140452334-chr7:140454838..140457503,3	K562	blood:

Variant related genes	Relation type
ENSG00000240889	Chromatin interaction
ENSG00000090266	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1009772	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10281975	0.91[EUR][1000 genomes]
rs11983228	0.89[EUR][1000 genomes]
rs13438418	0.91[EUR][1000 genomes]
rs1476868	0.82[ASN][1000 genomes]
rs17622717	0.82[ASN][1000 genomes]
rs17623204	0.82[ASN][1000 genomes]
rs17695341	0.82[ASN][1000 genomes]
rs17695623	0.82[ASN][1000 genomes]
rs17695707	0.82[ASN][1000 genomes]
rs17695995	0.80[ASN][1000 genomes]
rs1968140	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2930322	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41282721	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55720380	0.82[ASN][1000 genomes]
rs55875248	0.82[ASN][1000 genomes]
rs56055746	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56115934	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56347011	0.82[EUR][1000 genomes]
rs57143942	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57620608	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57675404	0.82[ASN][1000 genomes]
rs57725920	0.90[ASN][1000 genomes]
rs57846481	0.86[EUR][1000 genomes]
rs58233801	0.85[AFR][1000 genomes]
rs58554741	0.86[AFR][1000 genomes]
rs59183598	0.82[ASN][1000 genomes]
rs59232128	0.80[ASN][1000 genomes]
rs59477283	0.82[ASN][1000 genomes]
rs59816436	0.86[EUR][1000 genomes]
rs60081231	0.80[ASN][1000 genomes]
rs60088791	0.81[AFR][1000 genomes]
rs60144069	0.85[AFR][1000 genomes]
rs60251368	0.82[ASN][1000 genomes]
rs61142678	0.88[AFR][1000 genomes]
rs61421775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484288	0.82[ASN][1000 genomes]
rs62484291	0.82[ASN][1000 genomes]
rs62484294	0.82[ASN][1000 genomes]
rs62484295	0.82[ASN][1000 genomes]
rs62484299	0.82[ASN][1000 genomes]
rs62484300	0.82[ASN][1000 genomes]
rs62485366	0.80[ASN][1000 genomes]
rs62485368	0.80[ASN][1000 genomes]
rs62485369	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62485370	0.80[ASN][1000 genomes]
rs62485372	0.80[ASN][1000 genomes]
rs62485377	0.84[EUR][1000 genomes]
rs62485379	0.84[EUR][1000 genomes]
rs62485383	0.86[EUR][1000 genomes]
rs62487899	0.91[EUR][1000 genomes]
rs62487900	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62487901	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62487902	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62487904	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62487906	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62487911	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487912	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487913	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487914	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487916	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62487918	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62487920	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62487921	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62487923	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71645962	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71645993	0.91[EUR][1000 genomes]
rs73492596	0.92[AMR][1000 genomes]
rs73494523	0.81[AFR][1000 genomes]
rs7797753	0.86[AFR][1000 genomes]
rs7806794	0.85[ASN][1000 genomes]
rs7810757	0.91[EUR][1000 genomes]

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
rs56940988	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 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	chr7:140398600-140459400	Weak transcription	Brain Germinal Matrix	brain
5	chr7:140398600-140491800	Weak transcription	Fetal Brain Male	brain
6	chr7:140399400-140468200	Weak transcription	Right Ventricle	heart
7	chr7:140400000-140474000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:140404400-140452400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:140404800-140489000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:140404800-140517000	Weak transcription	Psoas Muscle	Psoas
11	chr7:140405200-140470800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr7:140405600-140472200	Weak transcription	Brain Substantia Nigra	brain
13	chr7:140406600-140472800	Weak transcription	Hela-S3	cervix
14	chr7:140407000-140454200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:140407000-140466800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:140407200-140454400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:140407200-140459200	Weak transcription	Fetal Lung	lung
18	chr7:140407200-140468400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:140415000-140454200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:140415000-140504400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:140415200-140466400	Weak transcription	Aorta	Aorta
22	chr7:140415200-140472000	Weak transcription	Lung	lung
23	chr7:140415200-140506600	Weak transcription	Gastric	stomach
24	chr7:140421800-140474000	Weak transcription	Brain Angular Gyrus	brain
25	chr7:140423800-140453000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:140424200-140468200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:140424400-140476600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr7:140425400-140468400	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:140426200-140467200	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:140426200-140473000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr7:140426600-140455800	Weak transcription	NH-A	brain
32	chr7:140428200-140489400	Weak transcription	Small Intestine	intestine
33	chr7:140428600-140476600	Weak transcription	NHDF-Ad	bronchial
34	chr7:140428800-140453800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr7:140429200-140459600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:140431200-140474200	Weak transcription	Esophagus	oesophagus
37	chr7:140436800-140468200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:140438200-140466800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:140438400-140482400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr7:140439000-140459200	Weak transcription	Fetal Stomach	stomach
41	chr7:140439000-140459400	Weak transcription	Fetal Muscle Leg	muscle
42	chr7:140439200-140458200	Weak transcription	Ovary	ovary
43	chr7:140439600-140474800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr7:140439800-140455400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr7:140440000-140453800	Weak transcription	Dnd41	blood
46	chr7:140440000-140454400	Weak transcription	Osteobl	bone
47	chr7:140440000-140468400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:140440000-140469600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr7:140440000-140472000	Weak transcription	Brain Anterior Caudate	brain
50	chr7:140440400-140476400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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