Variant report

Variant	rs2364397
Chromosome Location	chr7:140405706-140405707
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	chr7:140372745..140374926-chr7:140405563..140407158,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146966	Chromatin interaction
ENSG00000133597	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10228254	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10230071	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10230163	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10232557	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs10234502	0.82[CHD][hapmap];0.90[LWK][hapmap];0.92[YRI][hapmap]
rs10241711	1.00[CHB][hapmap]
rs10244133	0.90[LWK][hapmap];0.88[YRI][hapmap]
rs10258462	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10258465	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10269699	0.92[CHB][hapmap]
rs10272940	0.90[LWK][hapmap];0.88[YRI][hapmap]
rs10281173	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs10281508	0.90[LWK][hapmap];0.88[YRI][hapmap]
rs10282499	0.90[LWK][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs1042179	0.82[AFR][1000 genomes]
rs1046515	0.83[CHB][hapmap]
rs1140034	1.00[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.81[ASN][1000 genomes]
rs11768253	0.80[AFR][1000 genomes]
rs12375245	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs1267600	0.92[CHB][hapmap]
rs1267601	0.92[CHB][hapmap]
rs1267602	0.88[YRI][hapmap]
rs1267603	0.88[YRI][hapmap]
rs1267606	0.92[CHB][hapmap]
rs1267609	0.81[CHB][hapmap]
rs1267611	0.83[CHB][hapmap]
rs1267612	0.82[CHD][hapmap];0.90[LWK][hapmap];0.92[YRI][hapmap]
rs1267613	0.83[CHB][hapmap]
rs1267615	0.87[YRI][hapmap]
rs1267616	0.92[YRI][hapmap]
rs1267618	0.92[YRI][hapmap]
rs1267619	0.92[CHB][hapmap]
rs1267623	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs1267624	0.87[LWK][hapmap];0.92[YRI][hapmap]
rs1267625	0.90[LWK][hapmap];0.88[YRI][hapmap]
rs1267632	0.90[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs1267634	0.90[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap]
rs1267635	0.90[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap]
rs1267636	0.83[CHB][hapmap]
rs1267637	0.90[LWK][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs1267638	0.92[CHB][hapmap]
rs1267642	0.83[CHB][hapmap]
rs1267643	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1267644	0.83[CHB][hapmap]
rs1267645	0.80[AFR][1000 genomes]
rs1267646	0.90[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap]
rs1267647	0.90[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs1267649	0.92[CHB][hapmap]
rs1272419	0.80[AFR][1000 genomes]
rs1639675	0.92[CHB][hapmap]
rs1639678	0.92[CHB][hapmap]
rs1639679	0.83[CHB][hapmap]
rs17161666	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17161750	0.92[CHB][hapmap]
rs1733827	0.92[CHB][hapmap]
rs1733832	0.92[CHB][hapmap]
rs2109742	0.92[YRI][hapmap]
rs2364393	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2364394	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2364395	0.81[ASN][1000 genomes]
rs2364396	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[ASN][1000 genomes]
rs2364399	0.90[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2535946	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs2535951	0.92[CHB][hapmap]
rs2706774	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs2706775	0.82[CHD][hapmap];0.90[LWK][hapmap];0.92[YRI][hapmap]
rs28533681	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2907949	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2907950	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2930315	0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2930318	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2930319	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2930328	0.88[MKK][hapmap]
rs2930329	0.88[MKK][hapmap]
rs2968548	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968549	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2968550	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2968551	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968555	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2968558	0.81[ASN][1000 genomes]
rs2968559	0.94[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.81[ASN][1000 genomes]
rs3789806	0.96[YRI][hapmap]
rs4140846	0.85[YRI][hapmap]
rs4624945	0.81[ASN][1000 genomes]
rs4727011	0.83[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4727040	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs4727041	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs4727053	0.81[ASN][1000 genomes]
rs4727072	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6464036	0.92[CHB][hapmap]
rs6464037	0.90[LWK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs6464123	0.92[CHB][hapmap]
rs6464937	1.00[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.81[ASN][1000 genomes]
rs6947950	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs6953568	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6953658	0.80[AFR][1000 genomes]
rs6954652	0.90[LWK][hapmap];0.88[YRI][hapmap]
rs6964724	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs6966197	0.90[LWK][hapmap];0.88[YRI][hapmap]
rs6967652	0.90[CHB][hapmap]
rs6969779	0.81[ASN][1000 genomes]
rs6977834	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7357151	0.80[AFR][1000 genomes]
rs7776491	0.82[CHD][hapmap];0.90[LWK][hapmap];0.88[YRI][hapmap]
rs7791924	0.82[CHD][hapmap];0.90[LWK][hapmap];0.92[YRI][hapmap]
rs7792746	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7792984	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs7793758	0.82[CHD][hapmap];0.90[LWK][hapmap];0.87[YRI][hapmap]
rs7796827	0.88[YRI][hapmap]
rs7798031	0.90[LWK][hapmap];0.88[YRI][hapmap]
rs7798324	0.90[LWK][hapmap];0.92[YRI][hapmap]
rs7800472	0.90[LWK][hapmap];0.88[YRI][hapmap]
rs7801086	0.90[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs7803697	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2364397	BRAF	Cis_1M	lymphoblastoid	RTeQTL
rs2364397	NDUFB2	cis	lymphoblastoid	seeQTL
rs2364397	NDUFB2	Cis_1M	lymphoblastoid	RTeQTL
rs2364397	ADCK2	cis	cerebellum	SCAN

Chromatin state (count:122 , 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	chr7:140397800-140405800	Weak transcription	Aorta	Aorta
3	chr7:140397800-140406800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:140398000-140406000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:140398000-140406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:140398000-140408800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:140398000-140419400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:140398000-140466600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:140398200-140406000	Weak transcription	Fetal Lung	lung
10	chr7:140398200-140406000	Weak transcription	HSMM	muscle
11	chr7:140398200-140473800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:140398200-140492600	Weak transcription	Colonic Mucosa	Colon
13	chr7:140398400-140405800	Weak transcription	Fetal Kidney	kidney
14	chr7:140398400-140406000	Weak transcription	Stomach Mucosa	stomach
15	chr7:140398400-140408400	Weak transcription	NHDF-Ad	bronchial
16	chr7:140398400-140422000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr7:140398400-140432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:140398600-140414800	Weak transcription	Small Intestine	intestine
19	chr7:140398600-140459400	Weak transcription	Brain Germinal Matrix	brain
20	chr7:140398600-140491800	Weak transcription	Fetal Brain Male	brain
21	chr7:140399400-140407000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:140399400-140414200	Weak transcription	Gastric	stomach
23	chr7:140399400-140468200	Weak transcription	Right Ventricle	heart
24	chr7:140399600-140408000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:140399600-140443800	Weak transcription	Fetal Heart	heart
26	chr7:140400000-140474000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:140401200-140407000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:140402200-140407200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:140402200-140407200	Strong transcription	Primary T cells from cord blood	blood
30	chr7:140402200-140407200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:140402400-140407000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:140402400-140407200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr7:140402400-140407200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr7:140402400-140408200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:140402600-140406600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:140402600-140406800	Strong transcription	Liver	Liver
37	chr7:140402600-140407200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr7:140402600-140407200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr7:140402600-140407200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:140402600-140407200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:140402600-140407200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:140402600-140407200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:140402600-140407200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr7:140402600-140407200	Strong transcription	Fetal Intestine Large	intestine
45	chr7:140402600-140407200	Strong transcription	Fetal Intestine Small	intestine
46	chr7:140402600-140407200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr7:140402600-140407200	Strong transcription	Fetal Muscle Leg	muscle
48	chr7:140402600-140407200	Strong transcription	Fetal Stomach	stomach
49	chr7:140402600-140407200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr7:140402600-140407200	Strong transcription	Thymus	Thymus

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