Variant report

Variant	rs12129856
Chromosome Location	chr1:171470374-171470375
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171465256..171467403-chr1:171468400..171471374,3	MCF-7	breast:
2	chr1:171454829..171458429-chr1:171468344..171472224,4	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1055417	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913167	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119596	0.90[ASN][1000 genomes]
rs12131694	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12136576	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12137832	1.00[CHB][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12139715	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12142594	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12145045	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12145085	0.81[EUR][1000 genomes]
rs12146022	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12733939	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734261	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12759907	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183533	0.83[AFR][1000 genomes]
rs190198	0.83[AFR][1000 genomes]
rs2294292	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294293	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235471	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235472	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235488	0.84[EUR][1000 genomes]
rs235495	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs235498	0.84[EUR][1000 genomes]
rs235502	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs235507	0.84[EUR][1000 genomes]
rs235886	0.83[EUR][1000 genomes]
rs235892	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs235895	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs235899	0.83[AFR][1000 genomes]
rs235900	0.83[AFR][1000 genomes]
rs235901	0.83[AFR][1000 genomes]
rs235902	0.83[AFR][1000 genomes]
rs235903	0.83[AFR][1000 genomes]
rs235910	0.84[EUR][1000 genomes]
rs235911	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs235912	0.83[EUR][1000 genomes]
rs56207586	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71637410	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71637418	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71637419	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74122850	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534464	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7534557	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7538745	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS 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 miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv465639	chr1:171459507-171545051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv548190	chr1:171459507-171545051	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171456000-171481800	Weak transcription	Placenta	Placenta
2	chr1:171456200-171475000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:171456400-171471200	Weak transcription	Thymus	Thymus
4	chr1:171456400-171473000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:171456400-171481800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:171456400-171483600	Weak transcription	Fetal Intestine Large	intestine
7	chr1:171456800-171474800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:171457600-171471000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:171457800-171482000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:171457800-171482200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:171458200-171471000	Weak transcription	Fetal Brain Female	brain
12	chr1:171459000-171482000	Weak transcription	HMEC	breast
13	chr1:171460400-171471800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:171460800-171470600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:171460800-171481400	Weak transcription	HSMM	muscle
16	chr1:171461800-171470400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:171462600-171471200	Weak transcription	Right Atrium	heart
18	chr1:171462600-171478000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:171462600-171482400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:171463000-171483200	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:171464000-171475200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:171464000-171483200	Weak transcription	Esophagus	oesophagus
23	chr1:171464200-171471000	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:171464200-171474600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:171464200-171476000	Weak transcription	NHDF-Ad	bronchial
26	chr1:171464200-171476800	Weak transcription	Brain Angular Gyrus	brain
27	chr1:171464200-171481600	Weak transcription	NHEK	skin
28	chr1:171464400-171470600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:171464400-171470600	Weak transcription	Fetal Brain Male	brain
30	chr1:171464400-171475400	Weak transcription	NH-A	brain
31	chr1:171464600-171470400	Weak transcription	Brain Germinal Matrix	brain
32	chr1:171464600-171471200	Weak transcription	Brain Anterior Caudate	brain
33	chr1:171465000-171473400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:171465000-171475000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:171465000-171476200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:171465200-171470600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:171465200-171470600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:171465200-171472400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:171465200-171475200	Weak transcription	Osteobl	bone
40	chr1:171465200-171475400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:171465200-171481800	Weak transcription	HUVEC	blood vessel
42	chr1:171465200-171482200	Weak transcription	Fetal Lung	lung
43	chr1:171465200-171483200	Weak transcription	NHLF	lung
44	chr1:171465200-171483600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:171466200-171470600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:171466200-171475000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:171466200-171475600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:171466400-171475600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:171466600-171470800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:171466800-171470600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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