Variant report

Variant	rs2748168
Chromosome Location	chr6:38545942-38545943
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	chr6:38542008..38544985-chr6:38545718..38547507,2	K562	blood:
2	chr6:38544949..38547362-chr6:38668805..38671647,2	K562	blood:

Variant related genes	Relation type
ENSG00000124767	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12525759	0.89[JPT][hapmap]
rs16890826	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16890840	0.83[JPT][hapmap]
rs1699006	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1699013	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1699015	0.85[CEU][hapmap]
rs1699018	0.85[CEU][hapmap]
rs1699020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1739622	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1739625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1781739	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1781740	0.85[CEU][hapmap]
rs1781741	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1781742	0.88[CEU][hapmap]
rs2748166	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2748169	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2814891	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2814893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62396459	0.84[ASN][1000 genomes]
rs62399160	0.84[ASN][1000 genomes]
rs6458060	0.82[CEU][hapmap]
rs7769186	1.00[CEU][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38510600-38546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
4	chr6:38532400-38547800	Weak transcription	Fetal Kidney	kidney
5	chr6:38533200-38547000	Weak transcription	Aorta	Aorta
6	chr6:38534400-38561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:38534800-38547000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:38535400-38554600	Weak transcription	Fetal Stomach	stomach
9	chr6:38535600-38547000	Weak transcription	Brain Substantia Nigra	brain
10	chr6:38535600-38547000	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:38535600-38555400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:38535600-38555800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:38535600-38556000	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:38535600-38556000	Weak transcription	NHLF	lung
15	chr6:38535600-38557600	Weak transcription	HSMM	muscle
16	chr6:38535800-38547800	Weak transcription	Osteobl	bone
17	chr6:38535800-38548000	Weak transcription	Fetal Heart	heart
18	chr6:38535800-38559800	Weak transcription	Fetal Lung	lung
19	chr6:38535800-38560200	Weak transcription	NH-A	brain
20	chr6:38535800-38564000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:38535800-38578200	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:38536000-38546800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:38536200-38556000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:38536200-38559200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:38536400-38555800	Weak transcription	NHDF-Ad	bronchial
26	chr6:38536400-38560200	Weak transcription	Brain Angular Gyrus	brain
27	chr6:38536800-38566400	Weak transcription	Pancreas	Pancrea
28	chr6:38537000-38557200	Weak transcription	Thymus	Thymus
29	chr6:38538000-38566800	Weak transcription	Esophagus	oesophagus
30	chr6:38538200-38558600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:38538600-38548000	Weak transcription	Fetal Intestine Small	intestine
32	chr6:38538600-38561800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:38538600-38562000	Weak transcription	Brain Germinal Matrix	brain
34	chr6:38539800-38554800	Weak transcription	Lung	lung
35	chr6:38539800-38562800	Weak transcription	Fetal Thymus	thymus
36	chr6:38540000-38548000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:38540200-38547800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:38540400-38549000	Weak transcription	Dnd41	blood
39	chr6:38540400-38552600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:38540400-38557800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:38540400-38560000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:38540400-38561600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr6:38540400-38567800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr6:38540400-38569200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr6:38540600-38547000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:38540600-38559200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:38540600-38560000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:38541000-38565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:38541400-38568600	Weak transcription	Spleen	Spleen
50	chr6:38541600-38567000	Weak transcription	Small Intestine	intestine

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