Variant report

Variant	rs9378164
Chromosome Location	chr6:31643522-31643523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31600031..31602072-chr6:31643441..31645750,2	MCF-7	breast:
2	chr6:31640888..31643598-chr6:31665920..31668358,2	MCF-7	breast:
3	chr6:31642643..31644341-chr6:31742570..31744549,2	MCF-7	breast:
4	chr6:31628072..31629869-chr6:31642878..31645662,2	MCF-7	breast:
5	chr6:31643514..31645855-chr6:31830307..31832340,2	K562	blood:

Variant related genes	Relation type
ENSG00000204386	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000204439	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2272592	0.81[ASN][1000 genomes]
rs2280801	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2295663	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28732150	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28732154	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28732157	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28732158	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28895016	0.82[EUR][1000 genomes]
rs3131384	0.84[ASN][1000 genomes]
rs3993757	0.91[ASN][1000 genomes]
rs9368699	0.87[AMR][1000 genomes]
rs9378200	0.82[EUR][1000 genomes]
rs9380266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9391731	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9404941	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
15	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9378164	MICB	cis	multi-tissue	Pritchard
rs9378164	C6orf48	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31634800-31648200	Weak transcription	Right Atrium	heart
2	chr6:31635000-31643800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:31635200-31643600	Strong transcription	Fetal Muscle Trunk	muscle
4	chr6:31635400-31643600	Strong transcription	Primary T cells from cord blood	blood
5	chr6:31635400-31643600	Strong transcription	Brain Anterior Caudate	brain
6	chr6:31635600-31643800	Strong transcription	Thymus	Thymus
7	chr6:31635600-31644600	Strong transcription	Fetal Intestine Small	intestine
8	chr6:31635600-31644600	Strong transcription	Fetal Stomach	stomach
9	chr6:31636000-31648400	Weak transcription	Fetal Heart	heart
10	chr6:31636200-31643800	Strong transcription	Fetal Thymus	thymus
11	chr6:31636400-31643800	Strong transcription	Stomach Smooth Muscle	stomach
12	chr6:31637400-31643800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:31637400-31644200	Weak transcription	A549	lung
14	chr6:31637600-31648200	Weak transcription	Psoas Muscle	Psoas
15	chr6:31638400-31644400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:31638400-31648200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:31638800-31648000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr6:31639800-31646800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:31639800-31648400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:31639800-31648400	Weak transcription	Fetal Brain Male	brain
21	chr6:31640000-31643600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:31640200-31644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:31640200-31645000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:31640200-31648000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:31640200-31648200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:31640200-31648200	Weak transcription	Fetal Kidney	kidney
27	chr6:31640200-31648200	Weak transcription	Stomach Mucosa	stomach
28	chr6:31640200-31648200	Weak transcription	HUVEC	blood vessel
29	chr6:31640200-31648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:31640200-31648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:31640400-31648200	Weak transcription	NHDF-Ad	bronchial
32	chr6:31640800-31643600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:31640800-31643600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:31640800-31648000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:31640800-31648200	Weak transcription	Hela-S3	cervix
36	chr6:31640800-31648200	Weak transcription	HMEC	breast
37	chr6:31640800-31648400	Weak transcription	Small Intestine	intestine
38	chr6:31641200-31644000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:31641200-31648200	Weak transcription	Fetal Lung	lung
40	chr6:31641200-31648400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:31641400-31644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:31641400-31644200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr6:31641400-31644200	Weak transcription	Primary B cells from cord blood	blood
44	chr6:31641400-31644400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:31641400-31647200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:31641400-31647200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:31641400-31647800	Weak transcription	NHLF	lung
48	chr6:31641400-31648000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:31641400-31648000	Weak transcription	Brain Angular Gyrus	brain
50	chr6:31641400-31648000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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