Variant report

Variant	rs2509840
Chromosome Location	chr11:93461401-93461402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:93459822..93462778-chr11:93509047..93511510,2	K562	blood:
2	chr11:92966947..92969391-chr11:93461362..93463469,2	MCF-7	breast:
3	chr11:93461073..93462615-chr11:93516480..93518625,2	MCF-7	breast:
4	chr11:93459100..93466497-chr11:93514555..93520746,14	K562	blood:
5	chr11:93456003..93458881-chr11:93460219..93462347,2	MCF-7	breast:
6	chr11:93458749..93462343-chr11:93515783..93520848,6	K562	blood:
7	chr11:93460575..93462984-chr11:93526258..93528931,2	K562	blood:
8	chr11:93461112..93461952-chr6:27860440..27861039,2	NB4	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAF1D-1	chr11:93459820-93462971	NONHSAT023660

No data

Variant related genes	Relation type
ENSG00000042429	Chromatin interaction
ENSG00000166004	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000166012	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1011993	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10734163	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10741470	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10741471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10741472	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10741473	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10765621	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10765622	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10765624	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10765625	0.88[AMR][1000 genomes]
rs10765626	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10765627	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10765628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10765629	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10765631	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10831085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10831086	1.00[EUR][1000 genomes]
rs10831088	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10831092	0.82[AMR][1000 genomes]
rs11020471	1.00[CEU][hapmap]
rs11020477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11020493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11822965	1.00[CEU][hapmap]
rs12275974	1.00[CEU][hapmap]
rs12277621	0.82[ASN][1000 genomes]
rs12278291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12279657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12293939	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs16919267	0.87[ASN][1000 genomes]
rs17174449	0.87[ASN][1000 genomes]
rs1784203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1944099	1.00[CEU][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1944100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1944101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1944102	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1944103	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1944105	0.85[ASN][1000 genomes]
rs1944106	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1954994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2155245	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2155246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2155248	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288505	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2298706	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2298707	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2434986	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3737461	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3802770	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3802771	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3802773	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3802774	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3802775	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3819173	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs4237560	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4303195	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4303196	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4753095	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4753096	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4753097	1.00[CHB][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4753098	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4753099	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4753101	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4753488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4753489	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4753490	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4753491	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4753492	0.82[AMR][1000 genomes]
rs4753495	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs586655	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs59220317	0.87[ASN][1000 genomes]
rs60224981	0.82[ASN][1000 genomes]
rs60264207	0.87[ASN][1000 genomes]
rs60410024	0.82[ASN][1000 genomes]
rs61918554	0.82[ASN][1000 genomes]
rs623510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628916	1.00[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs630648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642984	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs643924	0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655279	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7101779	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7115167	0.87[ASN][1000 genomes]
rs7121150	1.00[EUR][1000 genomes]
rs7127033	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7129028	0.87[ASN][1000 genomes]
rs7130267	0.82[ASN][1000 genomes]
rs7926876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7929351	0.87[ASN][1000 genomes]
rs7930519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7937088	0.84[ASN][1000 genomes]
rs7937523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7939834	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7939847	1.00[CEU][hapmap]
rs7940153	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7949850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7951514	0.87[ASN][1000 genomes]
rs7952443	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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2509840	LOC374421	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93427000-93465800	Strong transcription	Hela-S3	cervix
2	chr11:93430800-93465400	Weak transcription	Stomach Mucosa	stomach
3	chr11:93442000-93463200	Weak transcription	Colonic Mucosa	Colon
4	chr11:93444000-93466400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:93444200-93462200	Weak transcription	Psoas Muscle	Psoas
6	chr11:93444800-93471000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:93445400-93465200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:93447600-93468000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:93448000-93465600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:93448600-93465400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr11:93449000-93462200	Weak transcription	Small Intestine	intestine
12	chr11:93449200-93462400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:93449200-93471800	Weak transcription	Right Atrium	heart
14	chr11:93449400-93461600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:93449400-93463800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:93449400-93465400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:93449600-93462200	Weak transcription	Spleen	Spleen
18	chr11:93449600-93462400	Weak transcription	Right Ventricle	heart
19	chr11:93449600-93471800	Weak transcription	Esophagus	oesophagus
20	chr11:93450000-93462200	Weak transcription	Pancreas	Pancrea
21	chr11:93450200-93461600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:93450600-93471800	Weak transcription	Gastric	stomach
23	chr11:93450600-93473000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:93451600-93469800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:93451600-93470800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr11:93451800-93461800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr11:93451800-93462000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:93451800-93466800	Strong transcription	Dnd41	blood
29	chr11:93452000-93461600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr11:93452000-93462000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:93453200-93468000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:93453400-93465200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr11:93453600-93468000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr11:93453800-93465200	Strong transcription	Fetal Intestine Large	intestine
35	chr11:93453800-93471200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr11:93453800-93471800	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:93453800-93471800	Strong transcription	Fetal Thymus	thymus
38	chr11:93453800-93472400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr11:93454000-93470400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:93454200-93467000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:93454400-93467800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:93454400-93469000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:93454400-93469400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr11:93454400-93469600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr11:93454400-93469800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:93454400-93470000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr11:93454400-93470800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr11:93454400-93471000	Strong transcription	Fetal Lung	lung
49	chr11:93454600-93471000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:93454600-93471000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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