Variant report

Variant	rs1619030
Chromosome Location	chr15:42459034-42459035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42452722..42455427-chr15:42457119..42459983,4	K562	blood:

Variant related genes	Relation type
ENSG00000166887	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10775126	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs10851407	0.85[EUR][1000 genomes]
rs10851408	0.85[EUR][1000 genomes]
rs10851409	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs11070370	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs11631917	0.85[EUR][1000 genomes]
rs11631983	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs12438562	0.83[EUR][1000 genomes]
rs12441642	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12441700	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12594162	0.85[EUR][1000 genomes]
rs12917101	0.85[EUR][1000 genomes]
rs1359003	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1359004	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs1624183	0.91[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1626437	0.81[JPT][hapmap]
rs1659212	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs1659213	0.82[CHB][hapmap]
rs1659217	0.83[EUR][1000 genomes]
rs1659218	0.82[CHB][hapmap]
rs1659219	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1659222	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1678985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678989	0.81[JPT][hapmap]
rs1678991	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678992	0.82[CHB][hapmap]
rs1678993	0.82[CHB][hapmap]
rs1679002	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679009	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679012	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1703750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1703754	0.91[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs1703755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1712418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1712421	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2138831	1.00[CEU][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs2289295	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs2412682	0.85[EUR][1000 genomes]
rs2412685	0.85[EUR][1000 genomes]
rs2412705	0.83[EUR][1000 genomes]
rs2620386	0.82[CHB][hapmap]
rs2918459	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs2918460	0.82[CHB][hapmap]
rs2918461	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs3743006	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs3850774	0.81[EUR][1000 genomes]
rs4329897	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes]
rs4923940	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs4923943	0.85[EUR][1000 genomes]
rs4924645	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs4924648	0.85[EUR][1000 genomes]
rs4924653	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs4924658	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs4924660	0.85[EUR][1000 genomes]
rs58313689	0.84[EUR][1000 genomes]
rs59132828	0.83[EUR][1000 genomes]
rs598360	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622442	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622714	0.81[ASN][1000 genomes]
rs624841	0.81[ASN][1000 genomes]
rs633934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493027	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs660126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678778	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs681029	0.91[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7175863	0.83[EUR][1000 genomes]
rs7177120	0.82[EUR][1000 genomes]
rs7179709	0.82[CHB][hapmap]
rs7181742	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs7183015	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs7183546	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs73400993	0.81[EUR][1000 genomes]
rs765830	0.83[EUR][1000 genomes]
rs8024732	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs8025601	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs8031315	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs8033080	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8036046	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036380	0.83[EUR][1000 genomes]
rs8036596	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs8037020	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs9672382	0.90[EUR][1000 genomes]
rs9920921	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS 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 miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1619030	C15orf23	cis	parietal	SCAN
rs1619030	MAP1A	cis	parietal	SCAN
rs1619030	CAPN3	cis	parietal	SCAN
rs1619030	SNAP23	cis	parietal	SCAN
rs1619030	FRMD5	cis	cerebellum	SCAN
rs1619030	C15orf63	cis	parietal	SCAN
rs1619030	CDAN1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42449000-42481800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:42449600-42468200	Strong transcription	Fetal Brain Female	brain
3	chr15:42450200-42468600	Strong transcription	Fetal Stomach	stomach
4	chr15:42450200-42472400	Strong transcription	Fetal Intestine Small	intestine
5	chr15:42450400-42468400	Strong transcription	Primary T cells from cord blood	blood
6	chr15:42450400-42468400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr15:42450400-42476600	Strong transcription	Fetal Muscle Leg	muscle
8	chr15:42450600-42460800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:42450600-42463400	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:42450600-42468000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:42450600-42468200	Strong transcription	Brain Germinal Matrix	brain
12	chr15:42450600-42479800	Weak transcription	Psoas Muscle	Psoas
13	chr15:42450600-42485000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:42450600-42486200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:42450600-42487400	Strong transcription	Primary B cells from cord blood	blood
16	chr15:42450800-42463400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr15:42450800-42471400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:42450800-42484000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:42450800-42485000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:42450800-42485200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:42451000-42460800	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr15:42451000-42460800	Strong transcription	HepG2	liver
23	chr15:42451000-42461000	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr15:42451000-42461000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:42451000-42461200	Strong transcription	Gastric	stomach
26	chr15:42451000-42461200	Strong transcription	Spleen	Spleen
27	chr15:42451000-42462000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:42451000-42462000	Strong transcription	Colonic Mucosa	Colon
29	chr15:42451000-42462400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:42451000-42462600	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr15:42451000-42463200	Strong transcription	Adipose Nuclei	Adipose
32	chr15:42451000-42463400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr15:42451000-42463400	Strong transcription	GM12878-XiMat	blood
34	chr15:42451000-42463600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:42451000-42466000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:42451000-42466000	Strong transcription	Colon Smooth Muscle	Colon
37	chr15:42451000-42466000	Strong transcription	Pancreas	Pancrea
38	chr15:42451000-42468600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:42451000-42471000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:42451000-42479600	Strong transcription	Liver	Liver
41	chr15:42451000-42484000	Strong transcription	Placenta	Placenta
42	chr15:42451000-42484400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:42451000-42484800	Strong transcription	Fetal Intestine Large	intestine
44	chr15:42451000-42484800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr15:42451000-42485000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:42451000-42485000	Strong transcription	Thymus	Thymus
47	chr15:42451000-42487600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr15:42451200-42459600	Strong transcription	Pancreatic Islets	Pancreatic Islet
49	chr15:42451200-42460600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr15:42451200-42461600	Strong transcription	Ovary	ovary

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