Variant report

Variant	rs2624834
Chromosome Location	chr3:50132131-50132132
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50131320..50133089-chr3:50157321..50159844,2	K562	blood:
2	chr3:50132011..50135142-chr3:50138027..50140510,3	K562	blood:
3	chr3:50126047..50129250-chr3:50131237..50134548,5	K562	blood:
4	chr3:50130138..50132585-chr3:50151323..50154093,2	K562	blood:
5	chr3:50126047..50131036-chr3:50131245..50135023,6	K562	blood:
6	chr3:50131279..50132784-chr3:50275487..50276987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114353	Chromatin interaction
ENSG00000003756	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10049087	0.81[JPT][hapmap]
rs1061474	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11130228	0.81[JPT][hapmap]
rs11130233	0.89[JPT][hapmap]
rs1138536	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11709573	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs12107768	0.97[ASN][1000 genomes]
rs12496973	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs12634780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13060128	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs13082703	0.82[ASN][1000 genomes]
rs17657664	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17657688	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2013208	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2230590	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2240326	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2240327	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2240328	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240329	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2247510	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2252833	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2280406	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2352969	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[ASN][1000 genomes]
rs2352984	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2353579	0.82[JPT][hapmap]
rs2526747	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2526748	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2526749	0.92[ASN][1000 genomes]
rs2526750	0.89[ASN][1000 genomes]
rs2526751	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2526754	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2624815	0.95[ASN][1000 genomes]
rs2624817	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624819	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2624821	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.83[ASN][1000 genomes]
rs2624822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2624826	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2624829	0.81[ASN][1000 genomes]
rs2624832	0.82[ASN][1000 genomes]
rs2624843	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2624847	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2624848	0.91[ASN][1000 genomes]
rs2624853	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2681776	0.82[ASN][1000 genomes]
rs2681779	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2856234	0.85[CHD][hapmap]
rs2856237	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2856238	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2883057	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs34312088	0.82[ASN][1000 genomes]
rs3774733	0.82[JPT][hapmap]
rs3774734	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3774759	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4688688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4688689	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4688690	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4688753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4688754	0.95[ASN][1000 genomes]
rs4688755	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4688758	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6446193	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6446194	0.89[ASN][1000 genomes]
rs6446195	0.95[ASN][1000 genomes]
rs6446197	0.90[ASN][1000 genomes]
rs6762477	0.88[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6765484	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6771546	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6772095	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6774354	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6792892	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6793528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6799579	0.97[ASN][1000 genomes]
rs6808044	0.90[ASN][1000 genomes]
rs7061	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7430334	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7613875	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7615206	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7621026	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7621352	0.82[JPT][hapmap]
rs7628058	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7634441	0.95[ASN][1000 genomes]
rs7648174	0.82[ASN][1000 genomes]
rs7650241	0.82[EUR][1000 genomes]
rs868891	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9311446	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs9682295	0.95[ASN][1000 genomes]
rs9814664	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs9844201	0.84[ASN][1000 genomes]
rs9861216	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs9866695	0.85[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2624834	NCKIPSD	cis	parietal	SCAN
rs2624834	IL17RB	cis	cerebellum	SCAN
rs2624834	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2624834	RBM6	cis	parietal	SCAN
rs2624834	CYB561D2	cis	cerebellum	SCAN
rs2624834	C3orf78	cis	parietal	SCAN
rs2624834	NCKIPSD	cis	cerebellum	SCAN
rs2624834	C3orf18	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50127400-50132800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:50127400-50150000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:50127800-50157800	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr3:50128000-50134600	Strong transcription	Esophagus	oesophagus
5	chr3:50128000-50152600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:50128000-50157800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:50128000-50158000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:50128000-50158000	Strong transcription	Fetal Muscle Trunk	muscle
9	chr3:50128200-50134600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:50128200-50135000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:50128200-50152800	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr3:50128200-50158800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:50128400-50148800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:50128400-50157800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:50128400-50158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:50128400-50158400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:50128400-50159000	Strong transcription	Lung	lung
18	chr3:50128600-50132400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:50128600-50134600	Strong transcription	Aorta	Aorta
20	chr3:50128600-50137400	Weak transcription	Right Atrium	heart
21	chr3:50128600-50137400	Strong transcription	HSMM	muscle
22	chr3:50128600-50137400	Strong transcription	HSMMtube	muscle
23	chr3:50128600-50138000	Strong transcription	Small Intestine	intestine
24	chr3:50128600-50141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:50128600-50148800	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:50128600-50156200	Strong transcription	Ovary	ovary
27	chr3:50128600-50158000	Strong transcription	NH-A	brain
28	chr3:50128600-50158400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:50128600-50158400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:50128600-50158600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:50128600-50158600	Strong transcription	Colonic Mucosa	Colon
32	chr3:50128600-50158800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:50128600-50158800	Strong transcription	Brain Germinal Matrix	brain
34	chr3:50128600-50158800	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr3:50128600-50159000	Strong transcription	Brain Angular Gyrus	brain
36	chr3:50128600-50159000	Strong transcription	Placenta	Placenta
37	chr3:50128600-50159000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:50128600-50159200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:50128600-50159200	Strong transcription	Liver	Liver
40	chr3:50128600-50159200	Strong transcription	NHEK	skin
41	chr3:50128600-50160400	Strong transcription	Fetal Thymus	thymus
42	chr3:50128800-50134600	Strong transcription	Fetal Kidney	kidney
43	chr3:50128800-50137400	Strong transcription	Fetal Lung	lung
44	chr3:50128800-50149000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:50128800-50156600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:50128800-50156600	Strong transcription	Brain Substantia Nigra	brain
47	chr3:50128800-50158600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:50128800-50158600	Strong transcription	HMEC	breast
49	chr3:50128800-50159000	Strong transcription	Brain Anterior Caudate	brain
50	chr3:50129000-50132400	Strong transcription	Rectal Mucosa Donor 31	rectum

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