Variant report

Variant	rs6905572
Chromosome Location	chr6:31731881-31731882
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31647104..31649460-chr6:31731403..31733722,2	MCF-7	breast:
2	chr6:31729872..31732091-chr6:31831679..31833339,2	K562	blood:
3	chr6:31706580..31708960-chr6:31728802..31732177,3	MCF-7	breast:
4	chr6:31513724..31516419-chr6:31731123..31734011,2	K562	blood:
5	chr6:31730833..31734412-chr6:31734807..31737911,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SAPCD1-1	chr6:31731397-31731936	NONHSAT108831

Variant related genes	Relation type
ENSG00000204410	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000204396	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000204385	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000255152	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000204428	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12529130	0.88[ASN][1000 genomes]
rs2075788	0.82[EUR][1000 genomes]
rs2075801	0.82[EUR][1000 genomes]
rs2293861	0.82[EUR][1000 genomes]
rs2299851	0.91[ASN][1000 genomes]
rs3749953	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs409558	0.81[EUR][1000 genomes]
rs4711277	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711279	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4947253	0.82[EUR][1000 genomes]
rs6921489	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs733539	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7757496	0.88[ASN][1000 genomes]
rs7764451	0.85[ASN][1000 genomes]
rs7764682	0.85[ASN][1000 genomes]
rs9767684	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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
18	nsv884429	chr6:31730356-31837066	Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
19	nsv884430	chr6:31731881-31800631	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6905572	DOM3Z	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 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	chr6:31708600-31732000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:31708600-31734400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:31708800-31737400	Weak transcription	Liver	Liver
5	chr6:31709000-31738200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr6:31709200-31737400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:31709600-31737400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:31715200-31734000	Weak transcription	Esophagus	oesophagus
9	chr6:31715400-31733800	Weak transcription	Ovary	ovary
10	chr6:31715400-31733800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:31715600-31733800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:31716600-31744000	Weak transcription	GM12878-XiMat	blood
13	chr6:31724600-31733000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:31725400-31732200	Strong transcription	Dnd41	blood
15	chr6:31725400-31732600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:31725400-31733400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:31725800-31737800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:31726000-31732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:31726000-31732400	Strong transcription	Thymus	Thymus
20	chr6:31727600-31734000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:31727600-31738400	Weak transcription	Primary T cells from cord blood	blood
22	chr6:31728000-31732800	Strong transcription	Fetal Thymus	thymus
23	chr6:31728200-31734000	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:31729000-31734000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:31729000-31736800	Weak transcription	Primary B cells from cord blood	blood
26	chr6:31729200-31742800	Weak transcription	A549	lung
27	chr6:31729800-31734000	Weak transcription	Fetal Lung	lung
28	chr6:31729800-31735200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr6:31729800-31737400	Weak transcription	Colonic Mucosa	Colon
30	chr6:31730200-31732200	Weak transcription	K562	blood
31	chr6:31730200-31734000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:31730400-31732400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr6:31730400-31732600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:31730400-31733800	Weak transcription	Brain Germinal Matrix	brain
35	chr6:31730400-31734000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:31730600-31732200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:31730600-31732200	Enhancers	HepG2	liver
38	chr6:31730600-31732400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:31730600-31732400	Genic enhancers	Fetal Muscle Leg	muscle
40	chr6:31730600-31732400	Enhancers	Placenta	Placenta
41	chr6:31730600-31733800	Weak transcription	Fetal Brain Female	brain
42	chr6:31730600-31736200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:31730600-31736800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:31730800-31732000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:31730800-31732200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:31730800-31732200	Enhancers	NHDF-Ad	bronchial
47	chr6:31730800-31732400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:31730800-31732400	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr6:31730800-31732600	Genic enhancers	Fetal Stomach	stomach
50	chr6:31730800-31732600	Enhancers	Placenta Amnion	Placenta Amnion

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