Variant report

Variant	rs11679431
Chromosome Location	chr2:128211219-128211220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:127958570..127959604-chr2:128210884..128211764,3	MCF-7	breast:
2	chr2:127954244..127955683-chr2:128210529..128212030,11	MCF-7	breast:
3	chr2:128143917..128147453-chr2:128209353..128212433,7	MCF-7	breast:
4	chr2:128027989..128028584-chr2:128211038..128211648,2	MCF-7	breast:
5	chr2:128205487..128208672-chr2:128208949..128211983,3	K562	blood:
6	chr2:128063086..128065825-chr2:128211149..128213069,2	MCF-7	breast:
7	chr2:128112789..128113667-chr2:128211064..128211727,2	MCF-7	breast:
8	chr2:128112156..128113664-chr2:128210673..128211919,7	MCF-7	breast:
9	chr2:128082160..128083806-chr2:128210715..128211781,9	MCF-7	breast:
10	chr2:127955147..127956099-chr2:128210616..128211593,2	MCF-7	breast:
11	chr2:128081799..128083189-chr2:128210681..128212115,13	MCF-7	breast:
12	chr2:128143601..128146614-chr2:128208941..128211937,3	MCF-7	breast:
13	chr2:128081920..128082830-chr2:128210667..128211822,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000169967	Chromatin interaction
ENSG00000236682	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10201047	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10496663	1.00[ASW][hapmap];0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs10928765	0.87[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs10928766	0.89[EUR][1000 genomes]
rs10928769	0.86[EUR][1000 genomes]
rs11680815	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11681225	1.00[ASW][hapmap];0.87[CEU][hapmap]
rs11682864	0.86[EUR][1000 genomes]
rs11690086	0.86[EUR][1000 genomes]
rs11892245	0.84[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs11900469	0.89[EUR][1000 genomes]
rs12053309	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs12233101	0.87[CEU][hapmap]
rs12618494	0.94[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12619972	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12620037	0.93[CEU][hapmap]
rs12623334	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13011041	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13389029	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1568277	0.87[EUR][1000 genomes]
rs1568279	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17015274	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015334	0.87[CEU][hapmap]
rs2288655	1.00[ASW][hapmap];0.87[CEU][hapmap]
rs3732205	0.86[EUR][1000 genomes]
rs3889307	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56106399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58880408	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62160265	0.88[EUR][1000 genomes]
rs62160266	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62160287	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62160288	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62160289	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62160291	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66609069	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6716489	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67495946	0.87[EUR][1000 genomes]
rs7586672	0.94[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs880933	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv524607	chr2:128196424-128218364	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11679431	AC068282.3	cis	Thyroid	GTEx
rs11679431	GYPC	cis	parietal	SCAN
rs11679431	AC068282.3	cis	Nerve Tibial	GTEx
rs11679431	AC068282.3	cis	Esophagus Mucosa	GTEx
rs11679431	AC068282.3	cis	Stomach	GTEx
rs11679431	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11679431	AC068282.3	cis	Artery Tibial	GTEx
rs11679431	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs11679431	AC068282.3	cis	lung	GTEx
rs11679431	AC068282.3	cis	Whole Blood	GTEx
rs11679431	AC068282.3	cis	Muscle Skeletal	GTEx
rs11679431	AC068282.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128196200-128211600	Weak transcription	Colonic Mucosa	Colon
2	chr2:128204800-128213000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:128204800-128225600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:128205400-128223600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:128205400-128223800	Weak transcription	Placenta	Placenta
6	chr2:128205800-128223600	Weak transcription	Thymus	Thymus
7	chr2:128205800-128223800	Weak transcription	Lung	lung
8	chr2:128206000-128224000	Weak transcription	Psoas Muscle	Psoas
9	chr2:128206200-128237800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:128206600-128212600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:128206600-128212600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:128206800-128216600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:128206800-128233600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:128207000-128221000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:128207400-128212800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:128207600-128212600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:128207800-128211400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:128207800-128212600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:128207800-128212800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:128208000-128212600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:128208400-128212600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:128208400-128212800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:128208400-128213200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:128208400-128238800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:128208600-128211400	Weak transcription	Fetal Intestine Small	intestine
26	chr2:128208800-128226000	Weak transcription	Brain Anterior Caudate	brain
27	chr2:128209000-128238000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:128209200-128212000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:128209200-128221000	Weak transcription	Fetal Stomach	stomach
30	chr2:128209200-128223600	Weak transcription	Primary B cells from cord blood	blood
31	chr2:128209200-128223600	Weak transcription	Aorta	Aorta
32	chr2:128209200-128225400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:128209200-128237600	Weak transcription	Adipose Nuclei	Adipose
34	chr2:128209400-128223600	Weak transcription	Spleen	Spleen
35	chr2:128209600-128214400	Weak transcription	HSMMtube	muscle
36	chr2:128210000-128212600	Weak transcription	Dnd41	blood
37	chr2:128210000-128221800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:128210000-128223600	Weak transcription	Brain Substantia Nigra	brain
39	chr2:128210000-128226400	Weak transcription	Esophagus	oesophagus
40	chr2:128210000-128227200	Weak transcription	Left Ventricle	heart
41	chr2:128210000-128237600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:128210200-128238000	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:128210400-128211600	Strong transcription	Brain Angular Gyrus	brain
44	chr2:128210400-128222200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:128210600-128211800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:128210600-128215400	Strong transcription	Primary T cells from cord blood	blood
47	chr2:128210600-128225200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:128210800-128211400	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr2:128210800-128211400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:128210800-128212000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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