Variant report

Variant	rs10230163
Chromosome Location	chr7:140406648-140406649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140372745..140374926-chr7:140405563..140407158,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133597	Chromatin interaction
ENSG00000146966	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10228254	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10230071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10258462	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10258465	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2364396	0.81[ASN][1000 genomes]
rs2364397	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28533681	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2907949	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2907950	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2930315	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2930318	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2930319	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2968548	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968549	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2968550	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2968551	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2968553	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2968555	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4727072	0.84[ASN][1000 genomes]
rs6953568	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6977834	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7803697	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10230163	NDUFB2	Cis_1M	lymphoblastoid	RTeQTL
rs10230163	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140397600-140407400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:140397800-140406800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:140398000-140406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:140398000-140408800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:140398000-140419400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:140398000-140466600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:140398200-140473800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:140398200-140492600	Weak transcription	Colonic Mucosa	Colon
9	chr7:140398400-140408400	Weak transcription	NHDF-Ad	bronchial
10	chr7:140398400-140422000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:140398400-140432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:140398600-140414800	Weak transcription	Small Intestine	intestine
13	chr7:140398600-140459400	Weak transcription	Brain Germinal Matrix	brain
14	chr7:140398600-140491800	Weak transcription	Fetal Brain Male	brain
15	chr7:140399400-140407000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:140399400-140414200	Weak transcription	Gastric	stomach
17	chr7:140399400-140468200	Weak transcription	Right Ventricle	heart
18	chr7:140399600-140408000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr7:140399600-140443800	Weak transcription	Fetal Heart	heart
20	chr7:140400000-140474000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:140401200-140407000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:140402200-140407200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:140402200-140407200	Strong transcription	Primary T cells from cord blood	blood
24	chr7:140402200-140407200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:140402400-140407000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:140402400-140407200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr7:140402400-140407200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr7:140402400-140408200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:140402600-140406800	Strong transcription	Liver	Liver
30	chr7:140402600-140407200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:140402600-140407200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:140402600-140407200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:140402600-140407200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:140402600-140407200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:140402600-140407200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr7:140402600-140407200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:140402600-140407200	Strong transcription	Fetal Intestine Large	intestine
38	chr7:140402600-140407200	Strong transcription	Fetal Intestine Small	intestine
39	chr7:140402600-140407200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr7:140402600-140407200	Strong transcription	Fetal Muscle Leg	muscle
41	chr7:140402600-140407200	Strong transcription	Fetal Stomach	stomach
42	chr7:140402600-140407200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr7:140402600-140407200	Strong transcription	Thymus	Thymus
44	chr7:140402600-140407200	Strong transcription	Dnd41	blood
45	chr7:140402600-140407400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:140402600-140407600	Strong transcription	Fetal Thymus	thymus
47	chr7:140402800-140407000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr7:140402800-140407000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:140402800-140407200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:140402800-140407200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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