Variant report

Variant	rs2930322
Chromosome Location	chr7:140424582-140424583
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140423472..140425930-chr7:140432737..140435210,2	K562	blood:
2	chr7:140424087..140425930-chr7:140432654..140434237,2	K562	blood:
3	chr7:140396427..140399298-chr7:140424412..140427398,2	K562	blood:
4	chr7:140394191..140397016-chr7:140424090..140426297,2	MCF-7	breast:
5	chr7:140396319..140397970-chr7:140423059..140425912,3	K562	blood:

Variant related genes	Relation type
ENSG00000240889	Chromatin interaction
ENSG00000090266	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1009772	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10488098	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1476868	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17622717	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17623204	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17695341	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17695623	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17695707	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17695935	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17695995	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1968140	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2075046	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs41282721	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4140846	1.00[JPT][hapmap]
rs55720380	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55875248	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56055746	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56115934	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56940988	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57143942	0.80[EUR][1000 genomes]
rs57620608	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57675404	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57725920	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59183598	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59232128	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59477283	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60081231	0.84[EUR][1000 genomes]
rs60251368	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61421775	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62484288	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62484291	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62484294	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62484295	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62484299	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62484300	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62485366	0.84[EUR][1000 genomes]
rs62485368	0.84[EUR][1000 genomes]
rs62485369	0.80[EUR][1000 genomes]
rs62485370	0.84[EUR][1000 genomes]
rs62485372	0.84[EUR][1000 genomes]
rs62485390	0.84[EUR][1000 genomes]
rs62487899	0.88[EUR][1000 genomes]
rs62487900	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487901	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487902	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487904	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487906	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487911	0.85[ASN][1000 genomes]
rs62487912	0.85[ASN][1000 genomes]
rs62487913	0.85[ASN][1000 genomes]
rs62487914	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62487916	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62487918	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62487920	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62487921	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62487923	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71645962	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71645993	0.88[EUR][1000 genomes]
rs722011	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
rs2930322	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 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	chr7:140404800-140427600	Weak transcription	HSMMtube	muscle
12	chr7:140404800-140489000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:140404800-140517000	Weak transcription	Psoas Muscle	Psoas
14	chr7:140405200-140470800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:140405600-140472200	Weak transcription	Brain Substantia Nigra	brain
16	chr7:140406600-140472800	Weak transcription	Hela-S3	cervix
17	chr7:140407000-140425600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:140407000-140425600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:140407000-140427400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:140407000-140427600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:140407000-140428800	Weak transcription	NHLF	lung
22	chr7:140407000-140454200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr7:140407000-140466800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:140407200-140424600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:140407200-140424600	Weak transcription	Fetal Intestine Large	intestine
26	chr7:140407200-140425400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:140407200-140425400	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:140407200-140425400	Weak transcription	Esophagus	oesophagus
29	chr7:140407200-140425400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr7:140407200-140425400	Weak transcription	NH-A	brain
31	chr7:140407200-140425400	Weak transcription	NHEK	skin
32	chr7:140407200-140425400	Weak transcription	Osteobl	bone
33	chr7:140407200-140425600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr7:140407200-140425600	Weak transcription	HSMM	muscle
35	chr7:140407200-140427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:140407200-140427600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:140407200-140428000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:140407200-140433600	Weak transcription	Adipose Nuclei	Adipose
39	chr7:140407200-140437600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:140407200-140438000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr7:140407200-140438200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr7:140407200-140438200	Weak transcription	Ovary	ovary
43	chr7:140407200-140438200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:140407200-140438200	Weak transcription	HepG2	liver
45	chr7:140407200-140438600	Weak transcription	Left Ventricle	heart
46	chr7:140407200-140438800	Weak transcription	Brain Anterior Caudate	brain
47	chr7:140407200-140445400	Weak transcription	Spleen	Spleen
48	chr7:140407200-140449800	Weak transcription	A549	lung
49	chr7:140407200-140450000	Weak transcription	Pancreas	Pancrea
50	chr7:140407200-140454400	Weak transcription	H1 Cell Line	embryonic stem cell

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