Variant report

Variant	rs10241711
Chromosome Location	chr7:140384809-140384810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140374106..140376810-chr7:140384000..140385788,2	MCF-7	breast:
2	chr7:140371967..140374109-chr7:140384008..140387242,3	MCF-7	breast:
3	chr7:140381162..140385646-chr7:140395412..140398383,5	K562	blood:
4	chr7:140379583..140384830-chr7:140386891..140389682,4	K562	blood:
5	chr7:140383432..140386974-chr7:140394481..140397895,4	MCF-7	breast:
6	chr7:140380762..140385974-chr7:140393437..140399128,8	K562	blood:

Variant related genes	Relation type
ENSG00000090266	Chromatin interaction
ENSG00000146966	Chromatin interaction
ENSG00000133597	Chromatin interaction
ENSG00000240889	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10242534	0.84[EUR][1000 genomes]
rs1046515	0.83[CHB][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1140034	0.83[CHB][hapmap]
rs12375245	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267600	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1267601	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1267606	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1267609	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1267611	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1267613	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1267614	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1267617	0.87[EUR][1000 genomes]
rs1267619	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1267633	0.80[EUR][1000 genomes]
rs1267636	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1267638	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1267639	0.84[EUR][1000 genomes]
rs1267640	0.87[EUR][1000 genomes]
rs1267642	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1267643	0.83[CHB][hapmap]
rs1267644	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1267649	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1270193	0.87[EUR][1000 genomes]
rs1639675	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1639678	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1639679	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs17161666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17161668	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17161737	0.80[EUR][1000 genomes]
rs17161750	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1733827	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1733832	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1812162	0.98[EUR][1000 genomes]
rs2245716	0.87[EUR][1000 genomes]
rs2364393	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs2364394	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs2364396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2364397	1.00[CHB][hapmap]
rs2364398	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2535951	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs28517771	0.88[ASN][1000 genomes]
rs28577882	0.87[EUR][1000 genomes]
rs2907950	0.83[ASN][1000 genomes]
rs2930315	0.85[ASN][1000 genomes]
rs2930318	0.85[ASN][1000 genomes]
rs2930319	0.85[ASN][1000 genomes]
rs2968549	0.84[ASN][1000 genomes]
rs2968550	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2968551	0.87[ASN][1000 genomes]
rs2968553	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2968555	0.83[ASN][1000 genomes]
rs2968559	0.83[CHB][hapmap]
rs4725799	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4727011	0.83[CHB][hapmap]
rs4727021	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4727036	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4727040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4727041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4727053	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464036	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6464123	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6464937	0.83[CHB][hapmap]
rs6464984	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6949396	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6962426	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6967652	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6969779	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6977834	0.84[ASN][1000 genomes]
rs73489531	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73489562	0.87[EUR][1000 genomes]
rs73491672	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73491871	0.87[EUR][1000 genomes]
rs73505645	0.88[ASN][1000 genomes]
rs73505647	0.85[ASN][1000 genomes]
rs7792746	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs7794857	0.81[ASN][1000 genomes]
rs7803697	1.00[CHB][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv3409803	chr7:140383844-140390406	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10241711	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140373600-140385400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:140373800-140395600	Weak transcription	NH-A	brain
3	chr7:140373800-140395800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:140373800-140396000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:140374000-140395800	Weak transcription	Fetal Lung	lung
6	chr7:140374000-140395800	Weak transcription	Right Atrium	heart
7	chr7:140374200-140395800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:140374200-140396000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr7:140374200-140396000	Weak transcription	Psoas Muscle	Psoas
10	chr7:140374400-140395600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:140374400-140396200	Weak transcription	Small Intestine	intestine
12	chr7:140374600-140395600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:140374600-140395600	Weak transcription	A549	lung
14	chr7:140374600-140395800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr7:140374600-140395800	Weak transcription	Fetal Kidney	kidney
16	chr7:140374800-140395800	Weak transcription	Stomach Mucosa	stomach
17	chr7:140375000-140385000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr7:140375400-140392200	Strong transcription	Primary T cells from cord blood	blood
19	chr7:140375400-140394600	Weak transcription	Osteobl	bone
20	chr7:140375400-140395400	Strong transcription	Fetal Stomach	stomach
21	chr7:140375400-140395600	Weak transcription	HMEC	breast
22	chr7:140375600-140395600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr7:140375600-140395600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr7:140375600-140395800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr7:140375800-140390200	Strong transcription	Fetal Thymus	thymus
26	chr7:140375800-140395600	Weak transcription	Fetal Brain Male	brain
27	chr7:140375800-140395800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:140375800-140395800	Weak transcription	NHDF-Ad	bronchial
29	chr7:140376000-140393200	Strong transcription	Placenta	Placenta
30	chr7:140376000-140395600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:140376000-140395800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr7:140376200-140393400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:140376400-140390200	Strong transcription	Dnd41	blood
34	chr7:140376600-140390200	Strong transcription	Stomach Smooth Muscle	stomach
35	chr7:140376600-140395800	Weak transcription	GM12878-XiMat	blood
36	chr7:140376800-140395600	Strong transcription	Fetal Intestine Small	intestine
37	chr7:140377400-140390200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr7:140377400-140390200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr7:140377400-140392800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr7:140377400-140394400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr7:140377600-140385400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:140377600-140390200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr7:140377600-140390400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr7:140377600-140393200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:140377800-140391800	Strong transcription	Spleen	Spleen
46	chr7:140377800-140394800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:140377800-140394800	Strong transcription	Thymus	Thymus
48	chr7:140378000-140390200	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr7:140378000-140390200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr7:140378000-140392200	Strong transcription	Lung	lung

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