Variant report

Variant	rs6449150
Chromosome Location	chr4:15589314-15589315
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr4:15589292-15589569	MCF10A-Er-Src	breast:	n/a	chr4:15589401-15589409 chr4:15589402-15589409
2	MAFK	chr4:15589303-15589518	HepG2	liver:	n/a	chr4:15589429-15589444
3	FOS	chr4:15589272-15589572	MCF10A-Er-Src	breast:	n/a	chr4:15589401-15589409 chr4:15589402-15589409
4	MAFK	chr4:15589302-15589478	Hela-S3	cervix:	n/a	chr4:15589429-15589444
5	FOS	chr4:15589282-15589574	MCF10A-Er-Src	breast:	n/a	chr4:15589401-15589409 chr4:15589402-15589409

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15587526..15589843-chr4:15593660..15596117,2	K562	blood:
2	chr4:15587802..15589843-chr4:15592356..15595160,2	K562	blood:

Variant related genes	Relation type
CC2D2A	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11723478	0.80[AFR][1000 genomes]
rs11726647	0.86[JPT][hapmap]
rs12642407	0.81[AFR][1000 genomes]
rs13106528	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13114491	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13122812	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13127507	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13131119	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13131285	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13138894	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13141724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13144428	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13150957	0.81[AFR][1000 genomes]
rs1468735	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1468736	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16892135	1.00[JPT][hapmap]
rs16892143	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16892156	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17476670	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17476831	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1786	0.81[ASW][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs2041672	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2041673	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28447067	0.81[AFR][1000 genomes]
rs28644177	0.81[AFR][1000 genomes]
rs3182730	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34155734	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34427409	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34473224	0.81[AFR][1000 genomes]
rs34559117	0.81[AFR][1000 genomes]
rs34599140	0.85[ASN][1000 genomes]
rs34831330	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34924677	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35151159	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35196224	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35258636	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35309200	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35461787	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756247	0.86[JPT][hapmap]
rs3775957	0.81[AFR][1000 genomes]
rs41417147	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4267734	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4301111	0.86[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs4326008	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4346644	0.81[AFR][1000 genomes]
rs4396986	0.81[ASW][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes]
rs4423870	0.86[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes]
rs4549375	0.86[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs4613560	0.85[ASN][1000 genomes]
rs6414764	0.86[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs66472670	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67047740	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67089836	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67222859	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67224550	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6815254	0.81[ASW][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.84[YRI][hapmap]
rs6823775	0.80[AFR][1000 genomes]
rs6824422	0.86[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes]
rs6825051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6825815	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6826058	0.81[ASW][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs6834359	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6835038	1.00[JPT][hapmap]
rs6839654	0.81[ASW][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.88[YRI][hapmap]
rs6844141	1.00[JPT][hapmap]
rs6848779	0.85[LWK][hapmap];0.88[YRI][hapmap]
rs6852735	0.85[JPT][hapmap];0.82[AFR][1000 genomes]
rs7699180	0.80[ASN][1000 genomes]
rs9994518	0.85[LWK][hapmap];0.92[YRI][hapmap]

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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6449150	LOC285550	cis	multi-tissue	Pritchard
rs6449150	C1QTNF7	cis	cerebellum	SCAN
rs6449150	FAM200B	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
2	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
3	chr4:15546000-15589600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
5	chr4:15554600-15601400	Weak transcription	A549	lung
6	chr4:15555800-15589400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:15556000-15603200	Weak transcription	Fetal Thymus	thymus
8	chr4:15564000-15600600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:15564400-15603200	Weak transcription	HMEC	breast
10	chr4:15564600-15603600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:15565400-15612600	Weak transcription	Brain Substantia Nigra	brain
12	chr4:15565400-15621400	Weak transcription	Esophagus	oesophagus
13	chr4:15565600-15604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:15565600-15611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:15565800-15605000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:15566200-15596800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:15568400-15655600	Weak transcription	Gastric	stomach
18	chr4:15568600-15589400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:15569600-15596400	Weak transcription	NHDF-Ad	bronchial
20	chr4:15569600-15603600	Weak transcription	Spleen	Spleen
21	chr4:15569600-15604200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:15570200-15601800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:15570600-15602000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:15570600-15602000	Weak transcription	Pancreas	Pancrea
25	chr4:15570800-15589600	Weak transcription	Lung	lung
26	chr4:15571000-15597200	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:15571400-15596000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:15572000-15593400	Weak transcription	Fetal Brain Male	brain
29	chr4:15572200-15591600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:15572200-15593600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:15572200-15595600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:15572200-15601200	Weak transcription	NHLF	lung
33	chr4:15572200-15601800	Weak transcription	Brain Angular Gyrus	brain
34	chr4:15572200-15601800	Weak transcription	NHEK	skin
35	chr4:15572200-15604000	Weak transcription	Primary T cells from cord blood	blood
36	chr4:15572200-15604200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:15572400-15596200	Weak transcription	Ovary	ovary
38	chr4:15573200-15603800	Weak transcription	Fetal Intestine Small	intestine
39	chr4:15574800-15593200	Weak transcription	Brain Germinal Matrix	brain
40	chr4:15575200-15618000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:15576400-15592000	Weak transcription	Fetal Muscle Leg	muscle
42	chr4:15577000-15593000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:15577800-15589600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:15577800-15599000	Weak transcription	Left Ventricle	heart
45	chr4:15577800-15602800	Weak transcription	Placenta	Placenta
46	chr4:15578000-15589400	Weak transcription	Fetal Intestine Large	intestine
47	chr4:15578000-15599000	Weak transcription	Aorta	Aorta
48	chr4:15578400-15593600	Weak transcription	Fetal Heart	heart
49	chr4:15579000-15599200	Weak transcription	Osteobl	bone
50	chr4:15579200-15598600	Weak transcription	Liver	Liver

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