Variant report

Variant	rs805294
Chromosome Location	chr6:31688217-31688218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31619268..31620861-chr6:31687198..31689564,2	MCF-7	breast:
2	chr6:31686048..31689889-chr6:31795401..31797897,4	MCF-7	breast:
3	chr6:31685534..31689967-chr6:31702544..31705523,6	MCF-7	breast:
4	chr6:31668227..31672274-chr6:31683898..31689448,8	MCF-7	breast:
5	chr6:31686463..31688392-chr6:31828032..31830692,2	K562	blood:

Variant related genes	Relation type
ENSG00000204444	Chromatin interaction
ENSG00000204388	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000266776	Chromatin interaction
ENSG00000204386	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs385306	0.99[ASN][1000 genomes]
rs707916	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs707917	0.81[ASN][1000 genomes]
rs707928	0.83[EUR][1000 genomes]
rs805257	0.81[AMR][1000 genomes]
rs805274	0.81[ASN][1000 genomes]
rs805277	0.82[ASN][1000 genomes]
rs805281	0.81[ASN][1000 genomes]
rs805282	0.82[ASN][1000 genomes]
rs805285	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs805286	0.98[ASN][1000 genomes]
rs805287	0.83[ASN][1000 genomes]
rs805293	0.85[AFR][1000 genomes]
rs805304	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805305	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805306	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
12	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
13	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
14	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
rs805294	AIF1	Cis_1M	lymphoblastoid	RTeQTL
rs805294	CSNK2B	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31671800-31695800	Weak transcription	Right Atrium	heart
2	chr6:31679400-31691200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:31682000-31692800	Weak transcription	HSMMtube	muscle
4	chr6:31682000-31693800	Weak transcription	Fetal Kidney	kidney
5	chr6:31682200-31693400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:31682400-31692000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:31682400-31693600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:31682400-31693600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:31682400-31696400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:31683000-31693400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:31683200-31693200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:31683200-31693400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:31683200-31696200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:31683400-31692800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:31683600-31689200	Weak transcription	Brain Germinal Matrix	brain
16	chr6:31683600-31689800	Weak transcription	Fetal Stomach	stomach
17	chr6:31683600-31690000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:31683600-31693800	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:31683800-31688800	Weak transcription	Fetal Brain Female	brain
20	chr6:31683800-31691200	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:31684000-31693400	Weak transcription	Fetal Lung	lung
22	chr6:31685200-31688800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:31685200-31688800	Enhancers	Stomach Mucosa	stomach
24	chr6:31685200-31688800	Enhancers	HMEC	breast
25	chr6:31685200-31689600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr6:31685800-31696200	Weak transcription	Brain Anterior Caudate	brain
27	chr6:31686000-31690800	Weak transcription	K562	blood
28	chr6:31686200-31693600	Weak transcription	Aorta	Aorta
29	chr6:31686400-31695600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:31686600-31688600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:31686800-31688600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:31686800-31689000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:31686800-31691200	Weak transcription	Fetal Intestine Small	intestine
34	chr6:31686800-31693800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:31686800-31693800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:31686800-31694000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:31686800-31696200	Weak transcription	Small Intestine	intestine
38	chr6:31687000-31688600	Enhancers	NHEK	skin
39	chr6:31687000-31692800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:31687000-31693200	Weak transcription	Lung	lung
41	chr6:31687000-31693800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:31687000-31694000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr6:31687000-31694800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:31687000-31695800	Weak transcription	Pancreas	Pancrea
45	chr6:31687200-31690000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:31687200-31691400	Weak transcription	Fetal Intestine Large	intestine
47	chr6:31687200-31693800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:31687200-31694000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:31687200-31694800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:31687400-31693600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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