Variant report

Variant	rs12990935
Chromosome Location	chr2:153470922-153470923
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10497113	1.00[CHB][hapmap]
rs10931263	1.00[CHB][hapmap]
rs10931271	1.00[CHB][hapmap]
rs11674911	1.00[CHB][hapmap]
rs11689419	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694512	0.85[EUR][1000 genomes]
rs11901227	1.00[CHB][hapmap]
rs12475871	1.00[CHB][hapmap]
rs12478681	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12693429	1.00[CHB][hapmap]
rs12989903	1.00[CHB][hapmap]
rs12999331	1.00[CHB][hapmap]
rs13014141	1.00[CHB][hapmap]
rs13017131	1.00[CHB][hapmap]
rs13023975	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1370499	1.00[CHB][hapmap]
rs16831440	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16831456	1.00[CHB][hapmap]
rs17328776	1.00[CHB][hapmap]
rs17400938	1.00[CHB][hapmap]
rs17400980	1.00[CHB][hapmap]
rs2083097	1.00[CHB][hapmap]
rs34469468	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3811568	1.00[CHB][hapmap]
rs66839581	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728189	1.00[CHB][hapmap]
rs6736003	1.00[CHB][hapmap]
rs6741131	0.82[CEU][hapmap]
rs7575441	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591868	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598878	1.00[CHB][hapmap]

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	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153423800-153471200	Weak transcription	Fetal Kidney	kidney
2	chr2:153434200-153473600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:153435400-153473200	Weak transcription	Right Ventricle	heart
4	chr2:153438400-153475400	Weak transcription	Pancreas	Pancrea
5	chr2:153442800-153471600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:153443000-153476400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:153451200-153476200	Weak transcription	Gastric	stomach
8	chr2:153451400-153473600	Weak transcription	Aorta	Aorta
9	chr2:153454800-153471800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:153454800-153473600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:153454800-153473600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:153454800-153496600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:153457200-153473200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:153457200-153505000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:153460000-153471400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:153462200-153474800	Weak transcription	Fetal Intestine Small	intestine
17	chr2:153463600-153479600	Strong transcription	Placenta	Placenta
18	chr2:153463800-153502800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:153464000-153479200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:153464000-153502800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:153464600-153480000	Strong transcription	NHEK	skin
22	chr2:153465600-153474000	Weak transcription	Fetal Brain Male	brain
23	chr2:153466000-153471800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:153467200-153504000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:153468000-153472200	Strong transcription	Fetal Brain Female	brain
26	chr2:153468000-153474200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:153468000-153480000	Strong transcription	HepG2	liver
28	chr2:153468000-153483200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:153468200-153477800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:153468200-153479400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:153468400-153471600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:153468400-153473200	Weak transcription	Fetal Intestine Large	intestine
33	chr2:153468400-153479200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:153468600-153479200	Strong transcription	HMEC	breast
35	chr2:153468600-153480400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:153468600-153495800	Weak transcription	Esophagus	oesophagus
37	chr2:153468800-153475000	Weak transcription	Hela-S3	cervix
38	chr2:153468800-153479000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:153468800-153492000	Weak transcription	Liver	Liver
40	chr2:153469000-153471200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr2:153469000-153471600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:153469000-153472400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:153469000-153473000	Weak transcription	Ovary	ovary
44	chr2:153469000-153473200	Weak transcription	HSMMtube	muscle
45	chr2:153469000-153473400	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:153469000-153473600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:153469000-153473800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:153469000-153474200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:153469000-153475600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:153469000-153493800	Weak transcription	Spleen	Spleen

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