Variant report

Variant	rs2293861
Chromosome Location	chr6:31711124-31711125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31710692-31711213	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:31709734-31711172	K562	blood:	n/a	n/a
3	POLR2A	chr6:31706108-31713361	K562	blood:	n/a	n/a
4	POLR2A	chr6:31705222-31711233	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31685179..31687517-chr6:31710314..31712214,2	MCF-7	breast:
2	chr6:31710678..31714958-chr6:31739473..31744061,4	MCF-7	breast:
3	chr6:31709722..31711347-chr6:31926698..31929061,2	K562	blood:

Variant related genes	Relation type
MSH5	TF binding region
CLIC1	TF binding region
ENSG00000204420	Chromatin interaction
ENSG00000204396	Chromatin interaction
ENSG00000204351	Chromatin interaction
ENSG00000204356	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2075788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075801	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130486	0.96[ASN][1000 genomes]
rs3749953	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3828922	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs409558	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6905572	0.82[EUR][1000 genomes]
rs9469051	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2293861	FKBP5	cis	cerebellum	SCAN
rs2293861	TBX10	trans	cerebellum	SCAN
rs2293861	MSH5	cis	multi-tissue	Pritchard
rs2293861	DOM3Z	Cis_1M	lymphoblastoid	RTeQTL
rs2293861	C6orf48	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31707400-31724600	Weak transcription	Fetal Heart	heart
2	chr6:31708200-31733800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:31708400-31711400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:31708400-31714800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:31708400-31715000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:31708400-31715000	Weak transcription	Esophagus	oesophagus
7	chr6:31708400-31715000	Weak transcription	Ovary	ovary
8	chr6:31708400-31715000	Weak transcription	Pancreas	Pancrea
9	chr6:31708400-31717600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:31708400-31727000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:31708400-31729600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:31708400-31731000	Weak transcription	HSMMtube	muscle
13	chr6:31708400-31731200	Weak transcription	Gastric	stomach
14	chr6:31708400-31731200	Weak transcription	Lung	lung
15	chr6:31708400-31731200	Weak transcription	Right Atrium	heart
16	chr6:31708600-31714800	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:31708600-31715000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:31708600-31715000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:31708600-31715200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:31708600-31717000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:31708600-31728200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:31708600-31729400	Weak transcription	Fetal Lung	lung
23	chr6:31708600-31731200	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:31708600-31732000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:31708600-31734400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:31708800-31711200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:31708800-31711600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:31708800-31713400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:31708800-31714600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:31708800-31714800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:31708800-31715000	Weak transcription	Fetal Brain Female	brain
32	chr6:31708800-31716200	Strong transcription	Fetal Stomach	stomach
33	chr6:31708800-31717000	Weak transcription	Small Intestine	intestine
34	chr6:31708800-31723200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:31708800-31727400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr6:31708800-31727600	Weak transcription	Spleen	Spleen
37	chr6:31708800-31731200	Weak transcription	Brain Anterior Caudate	brain
38	chr6:31708800-31737400	Weak transcription	Liver	Liver
39	chr6:31709000-31711600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:31709000-31711800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:31709000-31712000	Strong transcription	Fetal Muscle Leg	muscle
42	chr6:31709000-31712400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:31709000-31712600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr6:31709000-31713400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:31709000-31715000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:31709000-31718200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:31709000-31719000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:31709000-31720400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:31709000-31720400	Weak transcription	NH-A	brain
50	chr6:31709000-31720400	Weak transcription	NHDF-Ad	bronchial

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