Variant report

Variant	rs12215077
Chromosome Location	chr6:110052880-110052881
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:110047914..110050234-chr6:110051143..110053248,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10457195	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs10457203	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10499053	0.92[MKK][hapmap];0.93[YRI][hapmap]
rs11153213	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11153215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153216	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11752791	0.81[EUR][1000 genomes]
rs11754340	0.81[EUR][1000 genomes]
rs11755641	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs11968978	0.88[MKK][hapmap]
rs12190372	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12191353	0.84[EUR][1000 genomes]
rs12192268	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12192776	0.87[EUR][1000 genomes]
rs12193719	0.82[EUR][1000 genomes]
rs12194061	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs12194157	0.87[EUR][1000 genomes]
rs12197838	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12197950	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12201356	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12201444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12203993	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12204548	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12205140	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12205485	0.83[EUR][1000 genomes]
rs12208018	0.80[EUR][1000 genomes]
rs12210706	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12528392	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12528781	0.85[EUR][1000 genomes]
rs13198852	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13199109	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13199135	0.82[EUR][1000 genomes]
rs13201430	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs1322124	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1960325	0.81[EUR][1000 genomes]
rs1980591	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[EUR][1000 genomes]
rs2025147	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2025148	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2273752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799845	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3799849	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3899233	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4141930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4490694	0.81[EUR][1000 genomes]
rs4945833	0.81[EUR][1000 genomes]
rs4947016	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6568592	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6911700	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71541003	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs729888	0.81[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7341297	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7451512	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7767525	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs971434	0.93[YRI][hapmap]

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	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS 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	5 gene(s)	inside rSNPs	diseases
6	nsv5436	chr6:110052812-110097662	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12215077	AKD1	cis	cerebellum	SCAN
rs12215077	SMPD2	cis	multi-tissue	Pritchard
rs12215077	CD164	cis	parietal	SCAN
rs12215077	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12215077	SMPD2	cis	parietal	SCAN
rs12215077	FIG4	cis	parietal	SCAN
rs12215077	FIG4	cis	cerebellum	SCAN
rs12215077	AKD1	cis	parietal	SCAN
rs12215077	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
2	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
3	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
5	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:110024200-110056400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:110025000-110057000	Weak transcription	Fetal Thymus	thymus
9	chr6:110027000-110056400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:110028200-110057200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:110034400-110060800	Weak transcription	Fetal Stomach	stomach
14	chr6:110034600-110056400	Weak transcription	Fetal Brain Female	brain
15	chr6:110034600-110057000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:110034800-110059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
19	chr6:110035200-110056200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:110035200-110065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:110035400-110057800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
24	chr6:110035600-110056400	Weak transcription	Ovary	ovary
25	chr6:110035600-110057000	Weak transcription	Pancreas	Pancrea
26	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
27	chr6:110035800-110057000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:110035800-110065000	Weak transcription	HSMM	muscle
29	chr6:110036200-110056200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:110036600-110057000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
32	chr6:110037200-110056000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:110037200-110056000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:110037600-110057000	Weak transcription	Psoas Muscle	Psoas
35	chr6:110038000-110056400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:110038000-110057000	Weak transcription	Fetal Intestine Large	intestine
37	chr6:110038400-110056400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:110039000-110054600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:110039000-110056400	Weak transcription	Placenta	Placenta
40	chr6:110039000-110081000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr6:110039200-110057000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:110039200-110058800	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:110039600-110053400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr6:110039600-110056400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:110039600-110057000	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:110039800-110062000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:110040400-110056400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:110040800-110062000	Weak transcription	Thymus	Thymus
49	chr6:110041000-110056000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:110041000-110057000	Weak transcription	Esophagus	oesophagus

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