Variant report

Variant	rs6573978
Chromosome Location	chr14:71200932-71200933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71195704..71197706-chr14:71200302..71202313,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10129307	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1034769	0.90[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs10873241	0.81[AFR][1000 genomes]
rs12589737	0.90[CEU][hapmap]
rs12879569	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1476610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107666	0.90[CEU][hapmap]
rs2158526	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2158527	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2332455	0.84[AFR][1000 genomes]
rs2332458	0.90[CEU][hapmap]
rs3814872	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.89[TSI][hapmap];0.85[AFR][1000 genomes]
rs4141095	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4899367	0.94[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs4899368	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.84[TSI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4902852	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.82[LWK][hapmap];0.89[TSI][hapmap]
rs6573980	0.85[AFR][1000 genomes]
rs7140653	0.90[CEU][hapmap]
rs7152246	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7152516	0.90[CEU][hapmap];0.81[AFR][1000 genomes]
rs8006424	0.94[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs8007131	0.85[AFR][1000 genomes]
rs8011047	0.94[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8011507	0.84[AFR][1000 genomes]
rs8018294	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6573978	FAM71D	cis	cerebellum	SCAN
rs6573978	MAP3K9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71185800-71219200	Weak transcription	Stomach Mucosa	stomach
2	chr14:71186000-71221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:71186000-71221600	Weak transcription	Hela-S3	cervix
4	chr14:71189800-71209400	Strong transcription	Fetal Brain Female	brain
5	chr14:71190000-71214400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:71191400-71220000	Weak transcription	Fetal Brain Male	brain
7	chr14:71191600-71220200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:71192400-71220200	Weak transcription	Fetal Kidney	kidney
9	chr14:71192600-71221800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr14:71193400-71211400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr14:71193600-71210200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:71193800-71209400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr14:71193800-71209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr14:71194000-71208400	Weak transcription	Brain Substantia Nigra	brain
15	chr14:71194000-71222000	Weak transcription	HSMMtube	muscle
16	chr14:71194200-71209600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr14:71194400-71201800	Weak transcription	Right Atrium	heart
18	chr14:71194400-71210400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr14:71194400-71213400	Weak transcription	Psoas Muscle	Psoas
20	chr14:71194400-71221600	Weak transcription	Left Ventricle	heart
21	chr14:71194600-71218600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr14:71194600-71221600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr14:71195400-71201600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr14:71195600-71202200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr14:71195600-71209400	Strong transcription	Placenta	Placenta
26	chr14:71195600-71209600	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr14:71195600-71210000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr14:71196200-71201200	Strong transcription	Brain Germinal Matrix	brain
29	chr14:71196200-71209200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr14:71196200-71217000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr14:71196400-71201800	Strong transcription	Fetal Stomach	stomach
32	chr14:71196400-71202000	Strong transcription	Fetal Intestine Small	intestine
33	chr14:71196400-71209400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr14:71196600-71201600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr14:71196800-71206600	Weak transcription	Aorta	Aorta
36	chr14:71197000-71201400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr14:71197000-71228800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr14:71197400-71204600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr14:71197600-71217000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr14:71197800-71203800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr14:71198400-71201400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr14:71198400-71203000	Strong transcription	Primary T cells from cord blood	blood
43	chr14:71198400-71209400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr14:71198400-71223400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr14:71198600-71201600	Strong transcription	Gastric	stomach
46	chr14:71198600-71201800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr14:71198600-71201800	Strong transcription	HepG2	liver
48	chr14:71198800-71201200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr14:71198800-71201200	Strong transcription	Colonic Mucosa	Colon
50	chr14:71198800-71201600	Strong transcription	Lung	lung

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