Variant report

Variant	rs3767868
Chromosome Location	chr1:212607404-212607405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212541839..212544001-chr1:212606359..212607860,2	MCF-7	breast:
2	chr1:212587912..212590110-chr1:212604889..212609190,4	K562	blood:
3	chr1:212606631..212609505-chr1:212609658..212612237,5	K562	blood:
4	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
5	chr1:212606338..212608364-chr1:212730714..212733205,2	K562	blood:
6	chr1:212601837..212604261-chr1:212607082..212608866,2	K562	blood:
7	chr1:212606882..212608476-chr1:212631103..212632696,2	MCF-7	breast:
8	chr1:212607004..212608669-chr1:212617399..212619627,2	MCF-7	breast:
9	chr1:212604504..212608752-chr1:212780786..212783858,6	K562	blood:
10	chr1:212586060..212592297-chr1:212603893..212609565,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction
ENSG00000065600	Chromatin interaction
ENSG00000260805	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1056985	0.95[CHB][hapmap]
rs10863965	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs11119918	0.95[CHB][hapmap]
rs11119927	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11119932	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11119934	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs11119936	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11119937	0.83[AFR][1000 genomes]
rs11119940	1.00[MKK][hapmap]
rs11119941	1.00[MKK][hapmap]
rs11119951	1.00[MKK][hapmap]
rs11119953	1.00[MKK][hapmap]
rs12031941	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12033979	0.98[ASN][1000 genomes]
rs12119779	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12128965	0.95[CHB][hapmap]
rs12133582	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs12133636	0.95[CHB][hapmap]
rs12134599	0.95[CHB][hapmap]
rs12136095	0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap]
rs12141427	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12145484	0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap]
rs12239580	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12403586	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1342152	0.95[CHB][hapmap]
rs1388033	1.00[ASN][1000 genomes]
rs1388034	1.00[ASN][1000 genomes]
rs14123	0.95[CHB][hapmap];1.00[GIH][hapmap]
rs1808986	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1826214	1.00[MKK][hapmap]
rs2166155	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs2298115	0.95[CHB][hapmap]
rs3754144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767867	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3767872	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3820513	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4338424	1.00[ASN][1000 genomes]
rs4548507	0.87[ASN][1000 genomes]
rs4951446	0.82[AMR][1000 genomes]
rs4951447	1.00[MKK][hapmap]
rs4951448	1.00[MKK][hapmap]
rs4951596	1.00[ASN][1000 genomes]
rs4951597	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59001230	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs74138154	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	esv3389348	chr1:212605479-212607477	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3767868	FAM159A	trans	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212605600-212607600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:212605600-212607600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:212605800-212607600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:212606000-212607600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:212606000-212607600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:212606000-212607800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr1:212606600-212607600	Flanking Active TSS	Fetal Brain Female	brain
8	chr1:212606800-212607600	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr1:212606800-212607600	Enhancers	Fetal Brain Male	brain
10	chr1:212606800-212607600	Flanking Active TSS	Fetal Muscle Trunk	muscle
11	chr1:212606800-212607800	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr1:212606800-212607800	Flanking Active TSS	NHEK	skin
13	chr1:212606800-212608000	Flanking Active TSS	Dnd41	blood
14	chr1:212606800-212608000	Flanking Active TSS	K562	blood
15	chr1:212607000-212607600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:212607000-212607600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:212607000-212607600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:212607000-212607600	Enhancers	Primary B cells from peripheral blood	blood
19	chr1:212607000-212607600	Enhancers	Placenta	Placenta
20	chr1:212607000-212607600	Enhancers	Small Intestine	intestine
21	chr1:212607000-212607600	Enhancers	Stomach Mucosa	stomach
22	chr1:212607000-212607600	Flanking Active TSS	HepG2	liver
23	chr1:212607000-212607800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr1:212607000-212607800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:212607000-212607800	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:212607000-212607800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:212607000-212607800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:212607000-212607800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:212607000-212607800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr1:212607000-212607800	Enhancers	Fetal Thymus	thymus
31	chr1:212607000-212607800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr1:212607000-212607800	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr1:212607000-212607800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr1:212607000-212607800	Flanking Active TSS	GM12878-XiMat	blood
35	chr1:212607000-212608000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:212607000-212608000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:212607000-212608000	Enhancers	Esophagus	oesophagus
38	chr1:212607000-212608200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr1:212607000-212608200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:212607000-212608400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:212607000-212608400	Enhancers	Spleen	Spleen
42	chr1:212607000-212614000	Weak transcription	Gastric	stomach
43	chr1:212607000-212623400	Weak transcription	HSMMtube	muscle
44	chr1:212607200-212607600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:212607200-212607600	Weak transcription	Primary T cells from cord blood	blood
46	chr1:212607200-212607600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:212607200-212607600	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr1:212607200-212607600	Enhancers	Fetal Heart	heart
49	chr1:212607200-212607600	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr1:212607200-212607600	Enhancers	Thymus	Thymus

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