Variant report

Variant	rs12141288
Chromosome Location	chr1:241800205-241800206
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:241799353-241805428	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:241800110..241802719-chr1:241917456..241919841,2	K562	blood:
2	chr1:241799844..241805446-chr1:241909864..241915090,9	MCF-7	breast:
3	chr1:241681612..241683346-chr1:241799468..241801013,2	K562	blood:
4	chr1:241800150..241802189-chr1:241935454..241937787,2	MCF-7	breast:
5	chr1:241798094..241801033-chr1:242010173..242012572,2	MCF-7	breast:
6	chr1:241799429..241802453-chr1:241804405..241808572,4	MCF-7	breast:
7	chr1:241796724..241805103-chr1:242008052..242013159,15	K562	blood:
8	chr1:241799658..241805161-chr1:242010004..242013743,14	K562	blood:
9	chr1:241799259..241801184-chr1:241862624..241865531,2	K562	blood:

No data

Variant related genes	Relation type
CHML	TF binding region
ENSG00000162843	Chromatin interaction
ENSG00000091483	Chromatin interaction
ENSG00000174371	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12141693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144178	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3753223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765817	1.00[ASN][1000 genomes]
rs3765819	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs3765822	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765827	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819978	1.00[ASN][1000 genomes]
rs3819979	1.00[ASN][1000 genomes]
rs4660108	1.00[ASN][1000 genomes]
rs6660991	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6674268	1.00[ASN][1000 genomes]
rs73139006	1.00[ASN][1000 genomes]
rs73139008	1.00[ASN][1000 genomes]
rs73139010	1.00[ASN][1000 genomes]
rs73139033	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139034	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12141288	CHML	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241758800-241802400	Weak transcription	Right Ventricle	heart
2	chr1:241779400-241800400	Weak transcription	Osteobl	bone
3	chr1:241779400-241800600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:241779400-241801000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:241784400-241800600	Weak transcription	Fetal Brain Male	brain
6	chr1:241786200-241800400	Weak transcription	Psoas Muscle	Psoas
7	chr1:241786600-241800800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:241787800-241802400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:241788200-241800800	Weak transcription	Gastric	stomach
10	chr1:241788200-241801400	Weak transcription	Colonic Mucosa	Colon
11	chr1:241788200-241802800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:241788200-241802800	Weak transcription	Esophagus	oesophagus
13	chr1:241789200-241802800	Weak transcription	Pancreas	Pancrea
14	chr1:241791600-241800600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:241791600-241800800	Weak transcription	NHDF-Ad	bronchial
16	chr1:241791600-241801400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:241791600-241802200	Weak transcription	Adipose Nuclei	Adipose
18	chr1:241791600-241802200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:241791600-241802400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:241791800-241800600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:241791800-241800800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:241791800-241801000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:241791800-241801800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:241791800-241802200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:241791800-241802400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:241792000-241801000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:241792800-241800800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:241796600-241800400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:241796600-241800600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:241796800-241800600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:241797200-241800600	Weak transcription	Aorta	Aorta
32	chr1:241797200-241802400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:241797600-241801000	Weak transcription	Spleen	Spleen
34	chr1:241797800-241800400	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:241798400-241800800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:241798600-241800800	Enhancers	Primary T cells from cord blood	blood
37	chr1:241798800-241800400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:241798800-241801400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:241798800-241802200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:241798800-241802400	Weak transcription	Lung	lung
41	chr1:241799000-241800400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:241799000-241800400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:241799000-241800600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:241799000-241800600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:241799000-241800600	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:241799000-241800800	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr1:241799000-241800800	Weak transcription	Left Ventricle	heart
48	chr1:241799000-241801200	Weak transcription	Fetal Intestine Large	intestine
49	chr1:241799200-241800400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:241799200-241800400	Weak transcription	H1 Cell Line	embryonic stem cell

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