Variant report

Variant	rs6830714
Chromosome Location	chr4:166142783-166142784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10015885	0.87[EUR][1000 genomes]
rs10024370	0.87[EUR][1000 genomes]
rs11725167	0.85[CEU][hapmap]
rs11726531	0.91[CHB][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.81[YRI][hapmap]
rs12512319	1.00[JPT][hapmap]
rs16999615	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes]
rs17842697	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes]
rs17842699	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap]
rs2048604	0.96[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs28575657	0.93[EUR][1000 genomes]
rs3817246	0.92[JPT][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes]
rs3901797	0.91[EUR][1000 genomes]
rs3932270	0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs4690809	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4691180	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6536903	0.85[MEX][hapmap]
rs6828824	0.85[MEX][hapmap]
rs7662569	0.84[JPT][hapmap];0.81[YRI][hapmap]
rs7664299	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7685245	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7692029	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7698056	0.84[MEX][hapmap]
rs7699872	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS 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 target site	46 gene(s)	inside rSNPs	diseases
3	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv881168	chr4:165975122-166196438	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
6	nsv980271	chr4:166140782-166154486	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6830714	INTS12	trans	cerebellum	SCAN
rs6830714	TLL1	cis	parietal	SCAN
rs6830714	NAF1	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166129600-166154400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:166129600-166196800	Weak transcription	Pancreas	Pancrea
3	chr4:166130200-166150800	Weak transcription	Fetal Intestine Large	intestine
4	chr4:166130400-166143400	Weak transcription	Fetal Thymus	thymus
5	chr4:166130400-166143600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:166130400-166143600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:166130400-166143600	Weak transcription	HSMM	muscle
8	chr4:166130400-166176800	Weak transcription	Fetal Intestine Small	intestine
9	chr4:166130600-166142800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:166130600-166143200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:166130600-166146200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:166130600-166200800	Weak transcription	Lung	lung
13	chr4:166131200-166143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:166131400-166148600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:166131600-166143200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:166131600-166143400	Weak transcription	Dnd41	blood
17	chr4:166131600-166162800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:166131600-166165800	Weak transcription	Gastric	stomach
19	chr4:166131600-166196800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:166132000-166143600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:166132000-166156400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:166132200-166143600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:166132200-166143800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr4:166132200-166193800	Weak transcription	Fetal Brain Female	brain
25	chr4:166134000-166146000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:166134400-166143400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:166135600-166143600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:166135800-166152600	Weak transcription	Brain Germinal Matrix	brain
29	chr4:166135800-166159000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:166136000-166143600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr4:166136000-166176800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:166136800-166143600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:166137200-166143600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr4:166137600-166143400	Weak transcription	Adipose Nuclei	Adipose
35	chr4:166137600-166162800	Weak transcription	NH-A	brain
36	chr4:166137800-166143600	Weak transcription	Primary B cells from cord blood	blood
37	chr4:166137800-166143600	Weak transcription	Primary T cells from cord blood	blood
38	chr4:166137800-166194200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:166138000-166143400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr4:166138000-166143800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:166138000-166157200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:166138000-166161600	Weak transcription	HSMMtube	muscle
43	chr4:166138200-166143400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:166138200-166143600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr4:166138200-166168800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:166138400-166143400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr4:166138400-166185600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:166138800-166143600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr4:166138800-166143600	Weak transcription	GM12878-XiMat	blood
50	chr4:166141800-166142800	Enhancers	NHEK	skin

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