Variant report

Variant	rs4964787
Chromosome Location	chr12:104204071-104204072
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	chr12:104198690..104201561-chr12:104203107..104206456,4	K562	blood:
2	chr12:104198690..104200506-chr12:104204020..104206335,2	K562	blood:
3	chr12:104202254..104204379-chr12:104208308..104210775,2	MCF-7	breast:
4	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:
5	chr12:104195074..104198274-chr12:104203706..104206121,4	K562	blood:
6	chr12:104199856..104205672-chr12:104232098..104237727,8	K562	blood:
7	chr12:104202983..104205031-chr12:104211895..104214839,2	K562	blood:
8	chr12:104200580..104204661-chr12:104208067..104211223,3	K562	blood:
9	chr12:104198469..104201339-chr12:104203097..104205273,3	MCF-7	breast:
10	chr12:104201163..104204586-chr12:104223748..104226145,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000257754	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10082821	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778288	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778289	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861110	0.86[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs10861111	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10861113	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861114	0.91[EUR][1000 genomes]
rs10861115	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861116	0.86[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10861117	0.91[EUR][1000 genomes]
rs10861118	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861119	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111760	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11111780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11111790	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111802	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs11111803	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111806	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs11111807	0.91[EUR][1000 genomes]
rs12299784	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs12313259	0.86[CEU][hapmap];0.97[TSI][hapmap]
rs12320424	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs12368209	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs12369835	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426059	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1370782	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs1370783	0.90[EUR][1000 genomes]
rs17034657	0.86[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs3087891	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4964197	0.86[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs4964540	0.91[EUR][1000 genomes]
rs4964571	0.86[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4964574	0.91[EUR][1000 genomes]
rs4964605	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs6539102	0.91[EUR][1000 genomes]
rs7138889	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7315948	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175816	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4964787	RP11-341G23.4	cis	Whole Blood	GTEx
rs4964787	TU12B1-TY	cis	multi-tissue	Pritchard
rs4964787	IGF1	cis	parietal	SCAN
rs4964787	NT5DC3	cis	Whole Blood	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:104187400-104206800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:104187800-104212600	Weak transcription	GM12878-XiMat	blood
7	chr12:104190800-104204400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:104191000-104209800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr12:104191000-104211800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:104192600-104206600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:104193000-104217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:104194000-104206800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:104194400-104207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:104194600-104207000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:104194600-104214600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:104194600-104214800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:104194800-104207200	Weak transcription	Adipose Nuclei	Adipose
18	chr12:104194800-104215200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:104195000-104204400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:104195000-104205200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr12:104195000-104207800	Weak transcription	Fetal Lung	lung
22	chr12:104195000-104208600	Weak transcription	Left Ventricle	heart
23	chr12:104195000-104213800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:104195800-104208400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:104196400-104205000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:104196400-104213600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:104196400-104214800	Weak transcription	Brain Substantia Nigra	brain
28	chr12:104196400-104221800	Weak transcription	Brain Anterior Caudate	brain
29	chr12:104196600-104204200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:104196600-104206800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:104196600-104207800	Weak transcription	HSMMtube	muscle
32	chr12:104196600-104212800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:104196600-104213000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:104196800-104206400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:104196800-104206600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:104199200-104205200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:104199200-104211000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:104199200-104211800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:104199600-104204800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:104199600-104205000	Genic enhancers	Colon Smooth Muscle	Colon
41	chr12:104199600-104214600	Weak transcription	Esophagus	oesophagus
42	chr12:104200000-104214600	Weak transcription	Ovary	ovary
43	chr12:104200200-104204800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:104200200-104207000	Weak transcription	Liver	Liver
45	chr12:104200200-104216200	Weak transcription	NHDF-Ad	bronchial
46	chr12:104200400-104210000	Weak transcription	Hela-S3	cervix
47	chr12:104200800-104205600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:104200800-104207200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:104201000-104205200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:104201000-104205200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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