Variant report

Variant	rs2075801
Chromosome Location	chr6:31728267-31728268
allele	C/T
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	chr6:31728184-31728457	K562	blood:	n/a	n/a
2	POLR2A	chr6:31727512-31728836	K562	blood:	n/a	n/a
3	POLR2A	chr6:31725701-31732188	K562	blood:	n/a	n/a
4	POLR2A	chr6:31725734-31729224	K562	blood:	n/a	n/a
5	POLR2A	chr6:31727849-31728341	HL-60	blood:	n/a	n/a
6	POLR2A	chr6:31728119-31728671	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:31727486-31729173	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:31632965..31635691-chr6:31725815..31728371,2	MCF-7	breast:
2	chr6:31702464..31704574-chr6:31725937..31728566,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-850P	TF binding region
MSH5	TF binding region
SAPCD1	TF binding region
MSH5-SAPCD1	TF binding region
ENSG00000213719	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000204438	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2075788	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293861	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130486	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3749953	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3828922	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs409558	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6905572	0.82[EUR][1000 genomes]
rs9469051	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
10	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
11	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
12	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
13	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
14	esv2763547	chr6:31715882-31738478	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
15	nsv884426	chr6:31728102-31800868	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
16	nsv884427	chr6:31728102-31802465	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers 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 target site	152 gene(s)	inside rSNPs	diseases
17	nsv884428	chr6:31728102-31870326	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2075801	LY6G5C	cis	Whole Blood	GTEx
rs2075801	DOM3Z	Cis_1M	lymphoblastoid	RTeQTL
rs2075801	TBX10	trans	cerebellum	SCAN
rs2075801	FKBP5	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31708200-31733800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:31708400-31729600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:31708400-31731000	Weak transcription	HSMMtube	muscle
4	chr6:31708400-31731200	Weak transcription	Gastric	stomach
5	chr6:31708400-31731200	Weak transcription	Lung	lung
6	chr6:31708400-31731200	Weak transcription	Right Atrium	heart
7	chr6:31708600-31729400	Weak transcription	Fetal Lung	lung
8	chr6:31708600-31731200	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:31708600-31732000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:31708600-31734400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:31708800-31731200	Weak transcription	Brain Anterior Caudate	brain
12	chr6:31708800-31737400	Weak transcription	Liver	Liver
13	chr6:31709000-31738200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:31709200-31728400	Weak transcription	Stomach Mucosa	stomach
15	chr6:31709200-31737400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:31709600-31737400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:31710000-31731000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:31710600-31731200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:31710800-31731000	Weak transcription	HUVEC	blood vessel
20	chr6:31711200-31731400	Weak transcription	Fetal Kidney	kidney
21	chr6:31715200-31734000	Weak transcription	Esophagus	oesophagus
22	chr6:31715400-31733800	Weak transcription	Ovary	ovary
23	chr6:31715400-31733800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:31715600-31730800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:31715600-31733800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:31715800-31728400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:31716600-31744000	Weak transcription	GM12878-XiMat	blood
28	chr6:31717400-31728400	Weak transcription	HepG2	liver
29	chr6:31718600-31730800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:31721200-31731000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:31721400-31730800	Weak transcription	NHDF-Ad	bronchial
32	chr6:31721400-31731000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:31721400-31731000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:31721400-31731000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:31721400-31731000	Weak transcription	NH-A	brain
36	chr6:31724600-31733000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:31725000-31730600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:31725400-31730800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr6:31725400-31732200	Strong transcription	Dnd41	blood
40	chr6:31725400-31732600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:31725400-31733400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:31725600-31729200	Strong transcription	NHEK	skin
43	chr6:31725600-31730200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:31725600-31730600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:31725800-31730400	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr6:31725800-31730800	Strong transcription	Fetal Stomach	stomach
47	chr6:31725800-31731200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:31725800-31731400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr6:31725800-31737800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr6:31726000-31730200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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