Variant report

Variant	rs2025148
Chromosome Location	chr6:110027943-110027944
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	chr6:110024804..110028000-chr6:110359372..110362087,3	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10457192	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap]
rs10457194	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs10457195	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs10457203	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10499053	0.85[CHB][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap]
rs10782163	0.80[EUR][1000 genomes]
rs11153188	0.82[EUR][1000 genomes]
rs11153213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153214	0.94[ASN][1000 genomes]
rs11153215	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11153216	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11752791	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11754340	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11755641	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11968978	0.87[MKK][hapmap]
rs12190372	0.81[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12191353	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12192268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192776	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12193719	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12194061	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs12194157	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12197838	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12197950	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12201356	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12201444	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12203993	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12204548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12205140	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12205485	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12208018	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12208933	0.90[CHB][hapmap]
rs12210706	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12214639	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12215077	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]
rs12528392	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12528781	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13191066	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13198852	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13199109	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13199135	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13201430	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs13201947	0.80[EUR][1000 genomes]
rs13201951	0.83[EUR][1000 genomes]
rs1321328	0.90[CHB][hapmap]
rs1322124	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];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1960325	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1980591	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2025147	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2273752	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2357124	0.81[EUR][1000 genomes]
rs36131450	0.82[EUR][1000 genomes]
rs3799845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799849	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3899233	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4141930	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4490694	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4945833	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4947016	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6568592	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6911700	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6914498	0.90[CHB][hapmap]
rs71541003	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs729888	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7341297	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7451512	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs749517	0.80[EUR][1000 genomes]
rs7767525	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs971434	0.90[CHB][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2025148	AKD1	cis	cerebellum	SCAN
rs2025148	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs2025148	FIG4	cis	cerebellum	SCAN
rs2025148	SMPD2	cis	multi-tissue	Pritchard
rs2025148	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs2025148	CD164	cis	parietal	SCAN
rs2025148	AKD1	cis	lymphoblastoid	seeQTL
rs2025148	FIG4	cis	parietal	SCAN
rs2025148	SMPD2	cis	Whole Blood	GTEx
rs2025148	AKD1	cis	parietal	SCAN
rs2025148	SMPD2	cis	parietal	SCAN

Chromatin state (count:59 , 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	chr6:110013200-110034000	Weak transcription	Fetal Stomach	stomach
4	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
6	chr6:110013400-110038600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:110013800-110029600	Weak transcription	Fetal Lung	lung
10	chr6:110014000-110034400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:110014800-110034200	Weak transcription	Fetal Intestine Small	intestine
12	chr6:110018800-110034200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:110022200-110028200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr6:110022600-110029400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:110024200-110038800	Weak transcription	Thymus	Thymus
16	chr6:110024200-110056400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:110025000-110028000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:110025000-110034400	Weak transcription	Lung	lung
19	chr6:110025000-110057000	Weak transcription	Fetal Thymus	thymus
20	chr6:110025400-110029200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:110025800-110028400	Enhancers	Primary B cells from cord blood	blood
22	chr6:110026000-110028400	Enhancers	Primary T cells from cord blood	blood
23	chr6:110026200-110028000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr6:110026200-110028000	Enhancers	Brain Hippocampus Middle	brain
25	chr6:110026200-110028200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr6:110026400-110028200	Enhancers	Adipose Nuclei	Adipose
27	chr6:110026600-110028000	Enhancers	Primary B cells from peripheral blood	blood
28	chr6:110026600-110028000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:110026600-110028200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:110026600-110028200	Enhancers	Brain Anterior Caudate	brain
31	chr6:110026600-110028400	Enhancers	Brain Substantia Nigra	brain
32	chr6:110026800-110028400	Enhancers	Primary hematopoietic stem cells	blood
33	chr6:110027000-110028000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:110027000-110028400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:110027000-110038200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr6:110027000-110040400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:110027000-110052400	Weak transcription	Liver	Liver
38	chr6:110027000-110056400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:110027200-110028200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:110027200-110028200	Enhancers	Psoas Muscle	Psoas
41	chr6:110027400-110028000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:110027400-110028000	Enhancers	Brain Angular Gyrus	brain
43	chr6:110027400-110028000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:110027400-110028000	Enhancers	Colon Smooth Muscle	Colon
45	chr6:110027400-110028200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:110027400-110028200	Enhancers	Brain Cingulate Gyrus	brain
47	chr6:110027400-110028200	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr6:110027400-110028200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr6:110027600-110028000	Enhancers	H9 Cell Line	embryonic stem cell
50	chr6:110027600-110028200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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