Variant report

Variant	rs12506249
Chromosome Location	chr4:16190649-16190650
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:16188719..16191085-chr4:16191836..16194328,3	K562	blood:
2	chr4:16181639..16184226-chr4:16188641..16191282,2	K562	blood:

Variant related genes	Relation type
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10019399	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10034719	0.87[ASN][1000 genomes]
rs10516299	0.82[ASN][1000 genomes]
rs10939651	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10939652	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10939653	0.94[ASN][1000 genomes]
rs11724076	0.81[ASN][1000 genomes]
rs11724423	0.84[ASN][1000 genomes]
rs11731602	0.91[ASN][1000 genomes]
rs11736424	0.81[ASN][1000 genomes]
rs11736827	0.80[ASN][1000 genomes]
rs12504884	0.81[ASN][1000 genomes]
rs12506478	0.84[ASN][1000 genomes]
rs12513244	0.85[ASN][1000 genomes]
rs12643544	0.84[ASN][1000 genomes]
rs12646600	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1373112	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1619904	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1662650	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1662652	0.84[ASN][1000 genomes]
rs1662654	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1662656	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16893138	0.91[ASN][1000 genomes]
rs16893143	0.81[ASN][1000 genomes]
rs16893144	0.83[ASN][1000 genomes]
rs16893147	0.82[ASN][1000 genomes]
rs16893158	0.82[ASN][1000 genomes]
rs178450	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2044195	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28453363	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28618674	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28645901	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs317854	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs317855	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs317869	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs317870	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs317871	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs317872	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs317874	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs317875	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs317876	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs317877	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs317878	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35851218	0.81[ASN][1000 genomes]
rs4395495	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56218994	0.91[ASN][1000 genomes]
rs57089965	0.82[ASN][1000 genomes]
rs60460559	0.81[ASN][1000 genomes]
rs60768295	0.81[ASN][1000 genomes]
rs73128457	0.82[ASN][1000 genomes]
rs73130433	0.83[ASN][1000 genomes]
rs73130439	0.83[ASN][1000 genomes]
rs73130456	0.81[ASN][1000 genomes]
rs7657191	0.97[ASN][1000 genomes]
rs894639	0.89[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	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16161800-16193200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr4:16163200-16195800	Weak transcription	HMEC	breast
3	chr4:16164400-16195000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:16165000-16190800	Weak transcription	HUVEC	blood vessel
5	chr4:16168000-16208000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:16168000-16213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:16168200-16198000	Weak transcription	A549	lung
8	chr4:16168400-16194600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:16168400-16197800	Weak transcription	NHLF	lung
10	chr4:16168400-16198000	Weak transcription	NH-A	brain
11	chr4:16168600-16191000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:16168600-16198000	Weak transcription	NHEK	skin
13	chr4:16170400-16191400	Weak transcription	Colonic Mucosa	Colon
14	chr4:16170600-16191000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:16170800-16208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:16171400-16207200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:16171600-16191000	Weak transcription	Esophagus	oesophagus
18	chr4:16171600-16191600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:16171600-16194400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:16171600-16198000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:16172000-16191000	Weak transcription	Pancreas	Pancrea
22	chr4:16172000-16191000	Weak transcription	Small Intestine	intestine
23	chr4:16172000-16191000	Weak transcription	Spleen	Spleen
24	chr4:16172000-16198000	Weak transcription	HSMMtube	muscle
25	chr4:16172200-16190800	Weak transcription	Right Ventricle	heart
26	chr4:16172600-16191000	Weak transcription	Fetal Brain Female	brain
27	chr4:16172800-16190800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:16174400-16196800	Weak transcription	Stomach Mucosa	stomach
29	chr4:16176000-16191200	Weak transcription	NHDF-Ad	bronchial
30	chr4:16176200-16198000	Weak transcription	HSMM	muscle
31	chr4:16177000-16194000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:16178800-16191000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:16178800-16191400	Weak transcription	Gastric	stomach
34	chr4:16179200-16196000	Weak transcription	Fetal Heart	heart
35	chr4:16180800-16192600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr4:16181000-16190800	Weak transcription	Psoas Muscle	Psoas
37	chr4:16181000-16191000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:16181000-16197800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr4:16181000-16197800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr4:16181200-16190800	Weak transcription	Brain Angular Gyrus	brain
41	chr4:16181200-16190800	Weak transcription	Brain Hippocampus Middle	brain
42	chr4:16181200-16190800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
44	chr4:16181400-16190800	Weak transcription	Brain Substantia Nigra	brain
45	chr4:16181800-16191000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:16182600-16190800	Weak transcription	Brain Anterior Caudate	brain
47	chr4:16182600-16191000	Weak transcription	Thymus	Thymus
48	chr4:16182600-16191200	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:16182600-16194800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:16183000-16190800	Weak transcription	Stomach Smooth Muscle	stomach

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