Variant report

Variant	rs6964421
Chromosome Location	chr7:6520676-6520677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:6520365-6520781	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:6519345-6521609	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:6519412-6520792	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:6519335-6521689	IMR90	lung:	n/a	n/a
5	POLR2A	chr7:6519940-6521090	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:6520438-6520783	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6517704..6522059-chr7:6522068..6526480,12	K562	blood:
2	chr7:6515936..6521284-chr7:6521487..6524392,7	MCF-7	breast:
3	chr7:6499949..6501557-chr7:6518916..6521343,2	MCF-7	breast:
4	chr7:6500191..6503008-chr7:6519492..6521377,2	K562	blood:
5	chr7:6519667..6521215-chr7:6538954..6541938,2	K562	blood:
6	chr7:6509730..6517655-chr7:6520090..6524473,18	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269781	TF binding region
ENSG00000269781	Chromatin interaction
ENSG00000136240	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10951986	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs11766121	0.81[ASN][1000 genomes]
rs11975679	0.87[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs12113949	0.93[ASN][1000 genomes]
rs12702519	0.82[CHB][hapmap]
rs13233173	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs13239407	0.84[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs13240397	0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1403782	0.87[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs1523609	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2347780	0.81[ASN][1000 genomes]
rs4720677	0.88[ASN][1000 genomes]
rs4724811	0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs4724813	0.93[ASN][1000 genomes]
rs58885063	0.81[ASN][1000 genomes]
rs6463561	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs6463562	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs6463563	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6463564	0.95[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6463565	0.80[ASN][1000 genomes]
rs6463567	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6463568	0.86[ASN][1000 genomes]
rs6945009	0.95[ASN][1000 genomes]
rs6953782	0.96[ASN][1000 genomes]
rs6959389	0.81[ASN][1000 genomes]
rs6959558	0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6959768	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6960903	0.94[ASN][1000 genomes]
rs6961571	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs6963194	0.80[ASN][1000 genomes]
rs7782950	0.91[ASN][1000 genomes]
rs7786067	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7788091	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7799479	0.81[ASN][1000 genomes]
rs7800342	0.99[ASN][1000 genomes]
rs940243	0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.81[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	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv1824738	chr7:6431933-6554222	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv1825865	chr7:6431933-6554222	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv1026878	chr7:6490387-6592374	Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv830895	chr7:6514781-6722092	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv887429	chr7:6520676-6659509	Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
14	nsv887430	chr7:6520676-6668027	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6964421	RNF216L	cis	parietal	SCAN
rs6964421	CARD11	cis	cerebellum	SCAN
rs6964421	KDELR2	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6499600-6521800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:6503600-6522800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:6505000-6521400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr7:6507600-6522400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:6507800-6522600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:6508000-6522000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:6509200-6521400	Strong transcription	NHEK	skin
8	chr7:6509800-6522000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:6510200-6522200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:6510200-6522400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:6510200-6522600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:6511600-6521600	Weak transcription	Fetal Brain Male	brain
13	chr7:6512200-6520800	Weak transcription	Esophagus	oesophagus
14	chr7:6513200-6522400	Weak transcription	Aorta	Aorta
15	chr7:6513200-6522400	Weak transcription	Lung	lung
16	chr7:6513400-6521200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:6513400-6521200	Weak transcription	Brain Substantia Nigra	brain
18	chr7:6513600-6521200	Weak transcription	Fetal Lung	lung
19	chr7:6514000-6522400	Weak transcription	Thymus	Thymus
20	chr7:6514200-6522000	Genic enhancers	Fetal Muscle Leg	muscle
21	chr7:6514800-6521400	Weak transcription	HMEC	breast
22	chr7:6516400-6521800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:6516600-6521800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:6516800-6522000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr7:6517000-6521200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:6517000-6522000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:6517000-6522000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr7:6517000-6522600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:6517200-6521400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:6517200-6522000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr7:6517200-6522000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:6517200-6522000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr7:6517400-6521400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr7:6518000-6521600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr7:6518400-6521800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:6518800-6521000	Strong transcription	Fetal Brain Female	brain
37	chr7:6518800-6521800	Genic enhancers	Dnd41	blood
38	chr7:6518800-6522000	Enhancers	Ovary	ovary
39	chr7:6518800-6522400	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr7:6518800-6522400	Enhancers	Left Ventricle	heart
41	chr7:6519000-6522000	Weak transcription	Primary B cells from cord blood	blood
42	chr7:6519400-6520800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:6519400-6521200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr7:6519400-6521200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr7:6519400-6521600	Genic enhancers	Fetal Intestine Large	intestine
46	chr7:6519400-6521800	Genic enhancers	HSMM	muscle
47	chr7:6519400-6522000	Enhancers	Fetal Heart	heart
48	chr7:6519400-6522200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr7:6519400-6522400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:6519400-6522400	Enhancers	Stomach Mucosa	stomach

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