Variant report

Variant	rs840439
Chromosome Location	chr13:48624994-48624995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48610411..48612225-chr13:48624837..48627697,2	K562	blood:

Variant related genes	Relation type
ENSG00000136159	Chromatin interaction
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1104351	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11840968	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841315	0.82[EUR][1000 genomes]
rs12869161	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327656	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359616	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1752129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886977	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1998989	0.89[EUR][1000 genomes]
rs2025864	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094195	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094196	1.00[JPT][hapmap]
rs2104481	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148939	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2148940	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182373	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182378	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182785	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406694	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427704	0.86[EUR][1000 genomes]
rs4941618	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941620	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941624	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942720	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942723	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4942724	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972210	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972223	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972227	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973264	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561414	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561416	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561425	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561438	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7317685	0.83[AMR][1000 genomes]
rs7323702	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7325175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326381	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332363	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334801	0.90[EUR][1000 genomes]
rs7335797	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336170	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985469	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990541	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998786	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999270	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8001032	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001509	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002482	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002847	0.93[EUR][1000 genomes]
rs840428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840435	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.94[EUR][1000 genomes]
rs9526448	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526454	0.83[AMR][1000 genomes]
rs9526455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs9534884	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534934	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9534956	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534959	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9534966	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs9562792	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567988	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs840439	MED4	cis	uninvolved skin	skin_eQTL
rs840439	MED4	cis	lesional skin	skin_eQTL
rs840439	MED4	cis	normal skin	skin_eQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48612400-48625000	Weak transcription	Spleen	Spleen
2	chr13:48612600-48631600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:48612600-48640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:48612600-48645000	Weak transcription	Stomach Mucosa	stomach
5	chr13:48612800-48625000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr13:48612800-48628000	Weak transcription	Fetal Brain Male	brain
7	chr13:48612800-48640200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:48612800-48640400	Weak transcription	Psoas Muscle	Psoas
9	chr13:48613000-48640200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr13:48613000-48640400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr13:48613200-48626600	Weak transcription	Right Ventricle	heart
12	chr13:48613200-48629000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:48613200-48631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr13:48613200-48640400	Weak transcription	Fetal Heart	heart
15	chr13:48613200-48641600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr13:48613200-48642200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:48613400-48625800	Weak transcription	K562	blood
18	chr13:48613400-48641600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr13:48613400-48647000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr13:48613600-48625200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr13:48613600-48636400	Weak transcription	Hela-S3	cervix
22	chr13:48613600-48645000	Weak transcription	Small Intestine	intestine
23	chr13:48614400-48627600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr13:48614400-48628600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr13:48614400-48636400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr13:48614800-48628200	Strong transcription	Dnd41	blood
27	chr13:48616200-48625000	Weak transcription	Brain Hippocampus Middle	brain
28	chr13:48616200-48625400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr13:48616400-48626600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr13:48616400-48626600	Weak transcription	Pancreas	Pancrea
31	chr13:48616400-48642800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr13:48616600-48625400	Weak transcription	Brain Angular Gyrus	brain
33	chr13:48616600-48626600	Weak transcription	Fetal Lung	lung
34	chr13:48617600-48626600	Weak transcription	Esophagus	oesophagus
35	chr13:48618800-48625200	Weak transcription	HSMMtube	muscle
36	chr13:48618800-48626200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr13:48618800-48644800	Weak transcription	Colonic Mucosa	Colon
38	chr13:48619200-48628200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr13:48619600-48627400	Strong transcription	Fetal Thymus	thymus
40	chr13:48619600-48630200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr13:48619800-48628400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr13:48620000-48628400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:48620000-48629000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr13:48620000-48629000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr13:48620200-48628600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr13:48620200-48629600	Strong transcription	Fetal Intestine Large	intestine
47	chr13:48620200-48630400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr13:48620400-48627800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:48620800-48627800	Strong transcription	Fetal Muscle Leg	muscle
50	chr13:48621000-48629000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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