Variant report

Variant	rs2025147
Chromosome Location	chr6:110070767-110070768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10457203	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10499053	0.86[YRI][hapmap]
rs11153213	0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11153215	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11153216	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755641	0.81[CHB][hapmap]
rs12190372	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192268	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs12197838	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12201356	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12201444	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12203993	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204548	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210706	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12215077	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]
rs12528392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198852	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322124	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980591	0.81[CHB][hapmap]
rs2025148	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	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799845	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3799849	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3899233	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs4141930	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947016	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6568592	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6911700	0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71541003	0.81[EUR][1000 genomes]
rs729888	0.81[CHB][hapmap]
rs7341297	0.80[EUR][1000 genomes]
rs7451512	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971434	0.88[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	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	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
3	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
4	nsv886533	chr6:110067773-110126393	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2025147	SMPD2	cis	Whole Blood	GTEx
rs2025147	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs2025147	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
2	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
6	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
8	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
9	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
10	chr6:110039000-110081000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:110041400-110081000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:110042200-110088800	Weak transcription	Fetal Intestine Small	intestine
13	chr6:110042400-110089000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
15	chr6:110047200-110084000	Weak transcription	Small Intestine	intestine
16	chr6:110048600-110089800	Weak transcription	Fetal Kidney	kidney
17	chr6:110050400-110078400	Weak transcription	Fetal Brain Male	brain
18	chr6:110057200-110089000	Weak transcription	Fetal Brain Female	brain
19	chr6:110057400-110089000	Weak transcription	Esophagus	oesophagus
20	chr6:110057600-110086200	Weak transcription	Brain Anterior Caudate	brain
21	chr6:110058200-110087200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:110058200-110089000	Weak transcription	Lung	lung
23	chr6:110058400-110085000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:110058400-110089600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:110058800-110112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:110059200-110124000	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:110060000-110087800	Weak transcription	Fetal Thymus	thymus
28	chr6:110061200-110089200	Weak transcription	Pancreas	Pancrea
29	chr6:110062600-110089200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:110062800-110087400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:110062800-110088000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:110063000-110078000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:110065200-110084000	Weak transcription	Left Ventricle	heart
34	chr6:110065200-110089000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:110065200-110111200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:110065400-110094200	Weak transcription	Brain Substantia Nigra	brain
37	chr6:110065600-110073000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:110065600-110074200	Weak transcription	Fetal Intestine Large	intestine
39	chr6:110065600-110074400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:110065600-110077800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:110065600-110080800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:110065600-110084000	Weak transcription	Placenta	Placenta
43	chr6:110065600-110087200	Weak transcription	HSMMtube	muscle
44	chr6:110065600-110087400	Weak transcription	Fetal Stomach	stomach
45	chr6:110065600-110089000	Weak transcription	Gastric	stomach
46	chr6:110065600-110089200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:110065800-110071000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr6:110065800-110071400	Weak transcription	Ovary	ovary
49	chr6:110065800-110071600	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:110065800-110078000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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