Variant report

Variant	rs12041140
Chromosome Location	chr1:85834049-85834050
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	chr1:85832497..85835404-chr1:85838453..85841129,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12021849	0.89[AMR][1000 genomes]
rs12022538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12023006	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023795	0.89[AMR][1000 genomes]
rs12024405	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12029474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12033170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12033315	0.89[AMR][1000 genomes]
rs12033473	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12034481	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12036146	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038279	0.90[ASN][1000 genomes]
rs12039188	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042485	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12045545	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046433	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047139	0.81[ASN][1000 genomes]
rs12047220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048263	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12049582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2300638	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28847138	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3813603	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485987	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs58489234	0.85[EUR][1000 genomes];0.98[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
3	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85809200-85838400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:85814200-85839600	Weak transcription	Left Ventricle	heart
3	chr1:85816000-85839600	Weak transcription	Pancreas	Pancrea
4	chr1:85816600-85836800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:85823200-85836800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:85825000-85839000	Weak transcription	Aorta	Aorta
7	chr1:85826200-85838800	Weak transcription	Hela-S3	cervix
8	chr1:85827000-85834600	Enhancers	NHDF-Ad	bronchial
9	chr1:85827000-85837800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:85827200-85836800	Weak transcription	Adipose Nuclei	Adipose
11	chr1:85827200-85839000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:85827400-85839400	Weak transcription	Fetal Intestine Large	intestine
13	chr1:85827600-85836800	Weak transcription	HepG2	liver
14	chr1:85828000-85838800	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:85829400-85836800	Weak transcription	Brain Anterior Caudate	brain
16	chr1:85829400-85838400	Weak transcription	Fetal Kidney	kidney
17	chr1:85829600-85839000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:85830000-85835600	Weak transcription	Psoas Muscle	Psoas
19	chr1:85830800-85834200	Genic enhancers	HSMM	muscle
20	chr1:85831400-85834600	Enhancers	HUVEC	blood vessel
21	chr1:85831600-85834400	Enhancers	NHLF	lung
22	chr1:85831600-85836800	Weak transcription	Small Intestine	intestine
23	chr1:85831800-85836800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:85832200-85836600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:85832400-85834400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:85832600-85835600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:85832800-85835000	Weak transcription	A549	lung
28	chr1:85832800-85836400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:85832800-85838400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:85832800-85838800	Weak transcription	HSMMtube	muscle
31	chr1:85832800-85839600	Weak transcription	HMEC	breast
32	chr1:85833000-85834200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:85833000-85836000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:85833000-85838400	Weak transcription	NHEK	skin
35	chr1:85833200-85836600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:85833200-85837000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:85833400-85834600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:85833400-85836800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:85833400-85839000	Weak transcription	NH-A	brain
40	chr1:85833600-85834200	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:85833600-85834400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:85833600-85834800	Enhancers	Osteobl	bone
43	chr1:85833800-85834400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:85833800-85834800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:85833800-85834800	Enhancers	Fetal Intestine Small	intestine
46	chr1:85833800-85835000	Enhancers	Fetal Stomach	stomach
47	chr1:85834000-85834400	Enhancers	Stomach Mucosa	stomach
48	chr1:85834000-85834600	Enhancers	Duodenum Mucosa	Duodenum
49	chr1:85834000-85834800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:85834000-85834800	Enhancers	Fetal Muscle Leg	muscle

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