Variant report

Variant	rs11668179
Chromosome Location	chr19:39316194-39316195
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	chr19:39315714..39318484-chr19:39324884..39327703,2	K562	blood:
2	chr19:39307714..39309871-chr19:39312469..39316327,3	K562	blood:

Variant related genes	Relation type
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10403012	0.95[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10411480	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10411844	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10424892	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs10425464	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10426289	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1078734	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11671711	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12974488	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12977821	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1529713	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs2075587	0.81[AMR][1000 genomes]
rs2075588	0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2113123	0.86[JPT][hapmap]
rs2116852	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278010	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28496951	0.85[JPT][hapmap]
rs35829996	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4328569	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802928	0.82[EUR][1000 genomes]
rs7248208	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8104420	0.86[JPT][hapmap]
rs8108906	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs8110679	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs862454	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs862457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs862458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862460	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862461	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862462	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862463	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9419	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]

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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv911672	chr19:39252238-39318006	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11668179	ECH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39284000-39318200	Weak transcription	Fetal Kidney	kidney
2	chr19:39296200-39318200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39296400-39318000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:39296400-39318200	Weak transcription	NHEK	skin
5	chr19:39301400-39320200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:39304000-39317600	Weak transcription	HSMMtube	muscle
7	chr19:39304400-39316800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:39304400-39321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:39304600-39318200	Weak transcription	Osteobl	bone
10	chr19:39304800-39320800	Weak transcription	HSMM	muscle
11	chr19:39305200-39321600	Strong transcription	Fetal Stomach	stomach
12	chr19:39305400-39321000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:39305600-39318800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr19:39305600-39320400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:39305600-39321000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr19:39306400-39317800	Weak transcription	Small Intestine	intestine
17	chr19:39307400-39321800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:39308000-39317600	Weak transcription	Fetal Thymus	thymus
19	chr19:39308200-39320400	Weak transcription	NHLF	lung
20	chr19:39308400-39318200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:39308600-39318000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:39308800-39316600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:39308800-39318200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:39309000-39318000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr19:39309000-39318000	Weak transcription	Brain Angular Gyrus	brain
26	chr19:39309000-39318200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:39309000-39320400	Weak transcription	Hela-S3	cervix
28	chr19:39309200-39316600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:39310200-39317800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:39310400-39317800	Weak transcription	Dnd41	blood
31	chr19:39310400-39318000	Strong transcription	Adipose Nuclei	Adipose
32	chr19:39310400-39321600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:39311800-39316200	Weak transcription	Fetal Heart	heart
34	chr19:39311800-39317800	Weak transcription	HepG2	liver
35	chr19:39311800-39318000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:39311800-39321200	Weak transcription	Stomach Mucosa	stomach
37	chr19:39311800-39321400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr19:39312000-39317400	Weak transcription	Right Atrium	heart
39	chr19:39312400-39318000	Weak transcription	Gastric	stomach
40	chr19:39312600-39316200	Weak transcription	Brain Germinal Matrix	brain
41	chr19:39312600-39316400	Strong transcription	Liver	Liver
42	chr19:39312600-39316400	Weak transcription	Brain Anterior Caudate	brain
43	chr19:39312600-39316400	Weak transcription	Psoas Muscle	Psoas
44	chr19:39312600-39316800	Weak transcription	Fetal Brain Female	brain
45	chr19:39312600-39317200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr19:39312600-39318400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:39312600-39319800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr19:39312600-39320800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:39313400-39318000	Strong transcription	Fetal Muscle Leg	muscle
50	chr19:39313400-39318200	Strong transcription	Rectal Mucosa Donor 29	rectum

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