Variant report

Variant	rs4859408
Chromosome Location	chr4:76681582-76681583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76679544..76681900-chr4:76683172..76685751,3	K562	blood:
2	chr4:76648671..76650701-chr4:76681421..76683293,2	K562	blood:
3	chr4:76648234..76650693-chr4:76679507..76682408,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138757	Chromatin interaction
ENSG00000138768	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10016782	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10028291	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031352	0.84[AFR][1000 genomes]
rs10031616	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10033315	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10212995	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097112	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097113	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097122	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11727895	0.89[AFR][1000 genomes]
rs11728073	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730896	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932454	0.80[EUR][1000 genomes]
rs11938067	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11943497	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12505149	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508992	0.89[AFR][1000 genomes]
rs13102733	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13110602	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133144	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13133472	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13145290	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13147276	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16996019	0.80[YRI][hapmap]
rs17000786	0.93[ASW][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs186563	0.83[AFR][1000 genomes]
rs2047989	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2055997	0.81[JPT][hapmap]
rs2271472	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28680723	0.84[AFR][1000 genomes]
rs2869175	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2904018	0.84[ASN][1000 genomes]
rs324686	0.81[AFR][1000 genomes]
rs324688	0.83[AFR][1000 genomes]
rs324690	0.93[ASW][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs324691	0.83[AFR][1000 genomes]
rs324693	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs324696	0.83[AFR][1000 genomes]
rs324697	0.84[AFR][1000 genomes]
rs324698	0.81[AFR][1000 genomes]
rs324700	0.83[AFR][1000 genomes]
rs324701	0.83[AFR][1000 genomes]
rs324703	0.83[YRI][hapmap];0.87[AFR][1000 genomes]
rs324709	0.83[YRI][hapmap];0.87[AFR][1000 genomes]
rs324712	0.88[AFR][1000 genomes]
rs324713	0.89[AFR][1000 genomes]
rs324714	0.87[YRI][hapmap]
rs324722	0.89[AFR][1000 genomes]
rs324723	0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs324726	0.93[ASW][hapmap];0.93[LWK][hapmap];0.83[YRI][hapmap]
rs324727	0.93[ASW][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs324730	0.83[AFR][1000 genomes]
rs324731	0.82[AFR][1000 genomes]
rs324733	0.81[AFR][1000 genomes]
rs324735	0.93[ASW][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs324738	0.83[AFR][1000 genomes]
rs324740	0.93[ASW][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs3796479	0.84[CHD][hapmap]
rs3796481	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4262008	0.93[ASW][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs4446339	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859404	0.82[EUR][1000 genomes]
rs4859405	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4859406	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859409	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859549	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859552	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859554	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859555	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55664143	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62318556	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6531901	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6827016	0.83[AFR][1000 genomes]
rs6829993	0.83[EUR][1000 genomes]
rs6843016	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6845147	0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6846575	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847333	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7655464	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657198	0.85[AFR][1000 genomes]
rs7661037	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7665517	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693127	0.89[AFR][1000 genomes]
rs905954	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs987561	0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4859408	CCNG2	cis	cerebellum	SCAN
rs4859408	SCARB2	cis	parietal	SCAN
rs4859408	FAM47E	cis	parietal	SCAN
rs4859408	PPEF2	cis	parietal	SCAN
rs4859408	PAQR3	cis	cerebellum	SCAN
rs4859408	CXCL10	cis	parietal	SCAN
rs4859408	CDKL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76650800-76737800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:76652000-76696400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:76652400-76725000	Weak transcription	Hela-S3	cervix
4	chr4:76668400-76698600	Weak transcription	Fetal Brain Male	brain
5	chr4:76671000-76689400	Weak transcription	Fetal Heart	heart
6	chr4:76671000-76739400	Weak transcription	Stomach Mucosa	stomach
7	chr4:76671600-76707800	Weak transcription	Right Ventricle	heart
8	chr4:76672000-76692200	Weak transcription	Colonic Mucosa	Colon
9	chr4:76674800-76715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:76675000-76727400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:76675400-76683800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:76675400-76683800	Strong transcription	Liver	Liver
13	chr4:76675400-76686800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:76675400-76695400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:76676000-76696400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:76676200-76687600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:76676200-76689400	Weak transcription	NHLF	lung
18	chr4:76676200-76695200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:76676200-76695800	Weak transcription	Brain Substantia Nigra	brain
20	chr4:76676200-76696000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:76676400-76692000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:76676400-76695800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:76676400-76695800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:76676400-76696400	Weak transcription	Esophagus	oesophagus
25	chr4:76676400-76696400	Weak transcription	Pancreas	Pancrea
26	chr4:76676400-76696800	Weak transcription	NHEK	skin
27	chr4:76676400-76697200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:76676400-76704800	Weak transcription	Aorta	Aorta
29	chr4:76676400-76704800	Weak transcription	Gastric	stomach
30	chr4:76676400-76730600	Weak transcription	Spleen	Spleen
31	chr4:76676600-76692000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:76676600-76695800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:76676600-76695800	Weak transcription	Fetal Kidney	kidney
34	chr4:76676800-76682200	Weak transcription	Fetal Intestine Large	intestine
35	chr4:76676800-76683000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:76676800-76687400	Weak transcription	Primary T cells from cord blood	blood
37	chr4:76676800-76689600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:76676800-76690200	Weak transcription	Small Intestine	intestine
39	chr4:76676800-76691600	Weak transcription	HMEC	breast
40	chr4:76676800-76691800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:76676800-76692000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:76676800-76692400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr4:76676800-76692400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr4:76676800-76695200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:76676800-76695400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:76676800-76695400	Weak transcription	A549	lung
47	chr4:76676800-76695800	Weak transcription	Brain Germinal Matrix	brain
48	chr4:76676800-76695800	Weak transcription	Ovary	ovary
49	chr4:76676800-76695800	Weak transcription	Psoas Muscle	Psoas
50	chr4:76676800-76695800	Weak transcription	Thymus	Thymus

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