Variant report

Variant	rs10199517
Chromosome Location	chr2:30686945-30686946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30684348..30687151-chr2:30692032..30693911,2	K562	blood:
2	chr2:30677517..30682510-chr2:30682594..30687236,9	K562	blood:
3	chr2:30666329..30668432-chr2:30685565..30687906,2	K562	blood:
4	chr2:30668681..30671987-chr2:30686628..30689382,3	K562	blood:
5	chr2:30678530..30680872-chr2:30685623..30687236,2	K562	blood:

Variant related genes	Relation type
ENSG00000172954	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10180872	1.00[YRI][hapmap]
rs10195537	1.00[YRI][hapmap]
rs10203381	1.00[YRI][hapmap]
rs10207070	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs10207451	1.00[YRI][hapmap]
rs10208152	1.00[YRI][hapmap]
rs1026066	1.00[YRI][hapmap]
rs13034406	0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs13419683	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429099	1.00[YRI][hapmap]
rs13430761	0.92[YRI][hapmap]
rs1357849	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17322862	0.82[ASN][1000 genomes]
rs17322869	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs17322939	0.87[ASN][1000 genomes]
rs17394450	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1869431	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs1880540	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68085725	0.80[ASN][1000 genomes]
rs9808079	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10199517	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30671200-30688200	Weak transcription	HSMM	muscle
2	chr2:30671600-30688000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:30671600-30688200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:30671600-30694600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:30671600-30703400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:30671600-30704200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:30672000-30688000	Weak transcription	Fetal Lung	lung
8	chr2:30674200-30687400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:30678400-30704200	Weak transcription	Fetal Stomach	stomach
10	chr2:30678600-30688000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:30678600-30703800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:30678600-30710600	Weak transcription	NHLF	lung
13	chr2:30678800-30687800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:30679200-30688000	Weak transcription	Pancreas	Pancrea
15	chr2:30679400-30688000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:30679800-30687400	Weak transcription	Fetal Kidney	kidney
17	chr2:30679800-30688000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:30680400-30688000	Weak transcription	Thymus	Thymus
19	chr2:30680600-30688000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:30680600-30688000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:30681400-30688000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:30682200-30688000	Weak transcription	GM12878-XiMat	blood
23	chr2:30682400-30687400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:30682400-30687800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr2:30682400-30688000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:30682400-30688000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:30682400-30688000	Weak transcription	Fetal Intestine Large	intestine
28	chr2:30682400-30688000	Weak transcription	Right Atrium	heart
29	chr2:30682400-30693400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:30682400-30704400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:30682600-30687400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:30682600-30687400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:30682600-30687600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:30682600-30687800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:30682600-30687800	Weak transcription	Aorta	Aorta
36	chr2:30682600-30688000	Weak transcription	Gastric	stomach
37	chr2:30682600-30688000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:30682600-30688200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:30683200-30688000	Weak transcription	Psoas Muscle	Psoas
40	chr2:30683200-30692400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:30683400-30688000	Weak transcription	Right Ventricle	heart
42	chr2:30683600-30687000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:30683600-30687400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:30683800-30687600	Weak transcription	Ovary	ovary
45	chr2:30684000-30687800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:30684200-30687400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:30684600-30687200	Weak transcription	A549	lung
48	chr2:30685000-30687000	Enhancers	Primary B cells from peripheral blood	blood
49	chr2:30685200-30687000	Enhancers	Primary B cells from cord blood	blood
50	chr2:30685200-30689600	Enhancers	Primary T helper cells PMA-I stimulated	--

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