Variant report

Variant	rs12090507
Chromosome Location	chr1:173844544-173844545
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	chr1:173842881..173845710-chr1:173854372..173856048,2	K562	blood:
2	chr1:173844210..173845835-chr1:173854372..173856264,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10157215	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10157218	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10157371	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10157384	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10157684	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10158197	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10158568	1.00[EUR][1000 genomes]
rs10399912	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10489892	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10489893	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912668	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912674	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912681	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912683	0.84[AMR][1000 genomes]
rs10912687	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912688	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912693	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912699	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912700	1.00[EUR][1000 genomes]
rs10912701	1.00[EUR][1000 genomes]
rs10912707	1.00[EUR][1000 genomes]
rs10912708	1.00[EUR][1000 genomes]
rs10912711	1.00[EUR][1000 genomes]
rs10912712	1.00[EUR][1000 genomes]
rs10912725	1.00[EUR][1000 genomes]
rs1135333	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11487390	1.00[EUR][1000 genomes]
rs12057440	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12060967	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12061013	1.00[EUR][1000 genomes]
rs12062801	1.00[EUR][1000 genomes]
rs12063273	1.00[EUR][1000 genomes]
rs12063296	1.00[EUR][1000 genomes]
rs12064818	1.00[EUR][1000 genomes]
rs12065194	1.00[EUR][1000 genomes]
rs12067109	1.00[EUR][1000 genomes]
rs12067191	1.00[EUR][1000 genomes]
rs12068440	1.00[EUR][1000 genomes]
rs12069446	1.00[EUR][1000 genomes]
rs12072553	1.00[EUR][1000 genomes]
rs12073448	1.00[EUR][1000 genomes]
rs12078471	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12078645	1.00[EUR][1000 genomes]
rs12078817	1.00[EUR][1000 genomes]
rs12079240	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079315	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079650	1.00[EUR][1000 genomes]
rs12081137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12083064	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084213	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12086687	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12090440	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093624	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12094912	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12096013	1.00[EUR][1000 genomes]
rs1322773	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322781	1.00[EUR][1000 genomes]
rs1570385	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846395	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846398	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1903410	1.00[EUR][1000 genomes]
rs1903411	1.00[EUR][1000 genomes]
rs1956522	1.00[EUR][1000 genomes]
rs2227611	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2227622	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28853918	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4652225	0.91[AMR][1000 genomes]
rs56195767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57586767	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57820984	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59090917	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59332560	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60047664	1.00[EUR][1000 genomes]
rs6425256	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6684147	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6690869	1.00[EUR][1000 genomes]
rs73033131	1.00[EUR][1000 genomes]
rs74126415	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550107	1.00[EUR][1000 genomes]
rs874342	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425413	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425414	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425427	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425735	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425768	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs997165	1.00[EUR][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 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	chr1:173838200-173846600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:173838200-173854200	Weak transcription	Gastric	stomach
3	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
4	chr1:173838400-173844600	Weak transcription	Ovary	ovary
5	chr1:173838400-173844800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:173838400-173854200	Weak transcription	Esophagus	oesophagus
7	chr1:173838400-173854800	Weak transcription	Aorta	Aorta
8	chr1:173838400-173854800	Weak transcription	Right Ventricle	heart
9	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:173838600-173854800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:173838800-173855800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:173839000-173848400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:173839000-173850000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:173839000-173854800	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:173839000-173862800	Weak transcription	HMEC	breast
16	chr1:173839200-173850000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:173839200-173855000	Weak transcription	A549	lung
18	chr1:173839400-173847800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr1:173839400-173847800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:173839400-173849200	Strong transcription	Fetal Stomach	stomach
21	chr1:173839400-173850000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:173839600-173854600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:173839800-173845400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:173840000-173845400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:173840200-173845800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:173840200-173849600	Strong transcription	Placenta	Placenta
27	chr1:173840200-173854200	Weak transcription	Colonic Mucosa	Colon
28	chr1:173840200-173854800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:173840200-173856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:173840400-173845800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:173840400-173846400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:173840400-173846400	Weak transcription	Brain Germinal Matrix	brain
33	chr1:173840400-173846400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:173840400-173855000	Weak transcription	Psoas Muscle	Psoas
35	chr1:173840600-173844600	Weak transcription	NHEK	skin
36	chr1:173840600-173844800	Weak transcription	Fetal Intestine Small	intestine
37	chr1:173840600-173849400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:173840600-173854200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:173840800-173844600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:173840800-173844600	Weak transcription	Spleen	Spleen
41	chr1:173840800-173844800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:173840800-173844800	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:173840800-173844800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:173840800-173844800	Weak transcription	Lung	lung
45	chr1:173840800-173844800	Weak transcription	Pancreas	Pancrea
46	chr1:173840800-173844800	Weak transcription	Thymus	Thymus
47	chr1:173840800-173844800	Weak transcription	HSMMtube	muscle
48	chr1:173840800-173846600	Weak transcription	Fetal Thymus	thymus
49	chr1:173840800-173848400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:173840800-173854200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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