Variant report

Variant	rs4622456
Chromosome Location	chr15:52014958-52014959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52002992..52006343-chr15:52011753..52015104,3	K562	blood:
2	chr15:52013584..52016377-chr15:52029402..52031450,3	MCF-7	breast:
3	chr15:52014160..52016391-chr15:52017218..52019564,2	MCF-7	breast:
4	chr15:52013040..52016397-chr15:52016962..52020800,6	K562	blood:
5	chr15:51952049..51953706-chr15:52013977..52015547,2	K562	blood:

Variant related genes	Relation type
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10444798	0.88[AMR][1000 genomes]
rs10444823	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10775145	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11049	0.81[CEU][hapmap]
rs11070864	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070865	0.81[AMR][1000 genomes]
rs1133882	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11630084	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11632106	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11636345	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11638161	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11638766	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11638820	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12903707	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12905283	0.91[AMR][1000 genomes]
rs12917133	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1350174	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1466276	0.89[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1545602	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1811326	1.00[CEU][hapmap]
rs1867984	1.00[CEU][hapmap]
rs1902430	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1972689	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2006772	0.83[EUR][1000 genomes]
rs2014638	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2034857	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2034858	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2077743	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2168475	0.93[ASN][1000 genomes]
rs2264339	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2303443	1.00[CEU][hapmap]
rs2414116	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2414117	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2414119	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2436661	0.83[EUR][1000 genomes]
rs2554305	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2554306	0.85[EUR][1000 genomes]
rs2554307	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2554308	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2554332	1.00[CEU][hapmap]
rs2554336	1.00[CEU][hapmap]
rs2554349	0.83[CHB][hapmap]
rs2554354	0.82[CEU][hapmap]
rs2554355	0.82[CEU][hapmap]
rs2570224	1.00[CEU][hapmap]
rs2570228	1.00[CEU][hapmap]
rs2570231	0.82[EUR][1000 genomes]
rs2570233	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2570235	0.84[EUR][1000 genomes]
rs2570236	0.82[EUR][1000 genomes]
rs2570237	0.82[EUR][1000 genomes]
rs2570243	0.83[CEU][hapmap]
rs2570251	0.83[EUR][1000 genomes]
rs2570252	1.00[CEU][hapmap]
rs2570253	1.00[CEU][hapmap]
rs2570258	1.00[CEU][hapmap]
rs2623245	0.82[CEU][hapmap]
rs2623247	0.83[CEU][hapmap]
rs2623251	0.85[CEU][hapmap]
rs2623254	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2623259	1.00[CEU][hapmap]
rs2623263	0.85[CEU][hapmap]
rs3088312	0.82[AMR][1000 genomes]
rs3751596	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794530	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3794534	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794535	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794536	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4238383	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4502160	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4534783	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4774602	0.96[CEU][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775978	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775982	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4775983	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs526556	0.92[ASN][1000 genomes]
rs55843525	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55887408	0.85[EUR][1000 genomes]
rs6493515	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493518	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6493519	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493522	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6493523	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689884	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7163176	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165283	1.00[CEU][hapmap]
rs7165585	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7166110	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7166962	0.85[AMR][1000 genomes]
rs7168659	0.85[AMR][1000 genomes]
rs7171459	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7173375	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7174941	0.85[EUR][1000 genomes]
rs7181553	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7182917	0.82[EUR][1000 genomes]
rs8024081	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8024088	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8024589	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8026521	0.91[AMR][1000 genomes]
rs8027721	0.85[AMR][1000 genomes]
rs8028258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8028890	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8041268	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4622456	SCG3	cis	Frontal Cortex	GTEx
rs4622456	LYSMD2	cis	Muscle Skeletal	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:51974600-52016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:51975600-52017200	Weak transcription	Fetal Brain Male	brain
4	chr15:51984800-52018600	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:51990000-52016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:51991400-52018800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:51992200-52018800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:51993600-52016800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:51999800-52018200	Weak transcription	Fetal Stomach	stomach
10	chr15:52000800-52024000	Weak transcription	Gastric	stomach
11	chr15:52001000-52018600	Weak transcription	Pancreas	Pancrea
12	chr15:52002800-52016600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:52004400-52016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:52004800-52018600	Weak transcription	Spleen	Spleen
15	chr15:52006400-52018400	Weak transcription	Fetal Muscle Leg	muscle
16	chr15:52007000-52023400	Weak transcription	Brain Anterior Caudate	brain
17	chr15:52007600-52016800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:52007800-52016800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:52007800-52018200	Weak transcription	NHDF-Ad	bronchial
20	chr15:52008200-52023200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:52008400-52018400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:52008400-52023400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:52008800-52016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:52009000-52016600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:52010800-52018400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:52010800-52018400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:52011000-52017000	Weak transcription	Adipose Nuclei	Adipose
28	chr15:52011200-52018400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:52011200-52018600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:52011400-52016600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:52011400-52018800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:52011400-52023400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:52011600-52018400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:52011600-52023400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:52011800-52018200	Weak transcription	Hela-S3	cervix
36	chr15:52011800-52018200	Weak transcription	HMEC	breast
37	chr15:52012000-52016800	Strong transcription	Primary B cells from cord blood	blood
38	chr15:52012200-52015600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:52012400-52016600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:52012400-52017000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:52012400-52017200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr15:52012400-52024200	Weak transcription	Fetal Lung	lung
43	chr15:52012800-52015000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:52012800-52015600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:52012800-52017000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr15:52012800-52017200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr15:52012800-52017200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr15:52012800-52018400	Weak transcription	Ovary	ovary
49	chr15:52013000-52015000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:52013000-52017200	Strong transcription	Dnd41	blood

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