Variant report

Variant	rs12242330
Chromosome Location	chr10:98596053-98596054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:98593714..98596338-chr10:98621792..98624067,2	K562	blood:
2	chr10:98592318..98594800-chr10:98594886..98599322,5	MCF-7	breast:
3	chr10:98595510..98597192-chr10:98598664..98600998,2	MCF-7	breast:
4	chr10:98594492..98596521-chr10:98602633..98604736,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196233	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10437452	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11188937	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188939	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188940	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188947	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188954	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188955	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188956	0.93[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188959	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188967	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188971	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11188978	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12241405	0.83[EUR][1000 genomes]
rs12243551	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244490	0.95[EUR][1000 genomes]
rs12246067	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12247344	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249381	1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249427	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249891	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252424	1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252435	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12254525	0.83[GIH][hapmap]
rs12256424	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257413	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258355	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258469	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12259265	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261278	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261881	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262784	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263331	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264014	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12265242	0.86[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266068	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266185	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12267926	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268216	0.86[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268272	0.86[ASW][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376965	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112175	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112190	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104785	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183449	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28439735	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505353	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28758432	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394767	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56867696	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57408003	0.86[ASN][1000 genomes]
rs57501540	0.83[EUR][1000 genomes]
rs57716318	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270704	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58376960	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59751908	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59938221	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59999388	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60576681	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61492214	0.91[EUR][1000 genomes]
rs6584101	0.95[EUR][1000 genomes]
rs7071211	0.86[ASW][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs7072273	0.93[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082316	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082838	1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs7085822	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085851	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086875	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7090441	0.82[EUR][1000 genomes]
rs7090690	0.81[EUR][1000 genomes]
rs74153734	0.95[EUR][1000 genomes]
rs7893144	0.83[ASN][1000 genomes]
rs7893564	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894138	0.84[EUR][1000 genomes]
rs7894418	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895914	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7906294	0.84[EUR][1000 genomes]
rs7910221	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918085	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7920238	0.81[EUR][1000 genomes]
rs7921193	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921885	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv895910	chr10:98386483-98640994	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1053801	chr10:98506832-98610101	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	nsv825532	chr10:98567434-98618034	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12242330	CWF19L1	cis	parietal	SCAN
rs12242330	ENTPD7	cis	cerebellum	SCAN
rs12242330	CCNJ	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98593600-98596800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr10:98593800-98596200	Weak transcription	Gastric	stomach
3	chr10:98593800-98596400	Enhancers	Primary B cells from peripheral blood	blood
4	chr10:98593800-98596600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr10:98593800-98596600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr10:98593800-98596800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr10:98593800-98597000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr10:98593800-98599600	Weak transcription	Lung	lung
9	chr10:98593800-98600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:98593800-98600600	Weak transcription	Esophagus	oesophagus
11	chr10:98593800-98601800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr10:98593800-98602800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr10:98593800-98606800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:98593800-98624200	Weak transcription	Colonic Mucosa	Colon
15	chr10:98594000-98596400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr10:98594000-98596400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr10:98594000-98597800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:98594000-98604200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr10:98594200-98596200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr10:98594200-98596600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr10:98594200-98596600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:98594200-98596600	Enhancers	Hela-S3	cervix
23	chr10:98594200-98599200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr10:98594200-98600600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:98594200-98610200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr10:98594200-98610800	Weak transcription	Fetal Thymus	thymus
27	chr10:98594200-98639400	Weak transcription	Thymus	Thymus
28	chr10:98594400-98596200	Enhancers	Fetal Brain Male	brain
29	chr10:98594400-98596400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr10:98594400-98596600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:98594400-98596600	Enhancers	Brain Cingulate Gyrus	brain
32	chr10:98594400-98596600	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr10:98594400-98596600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr10:98594400-98596600	Enhancers	A549	lung
35	chr10:98594400-98596600	Enhancers	Osteobl	bone
36	chr10:98594400-98596800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr10:98594400-98596800	Enhancers	Liver	Liver
38	chr10:98594400-98596800	Enhancers	Brain Hippocampus Middle	brain
39	chr10:98594400-98599600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:98594400-98618800	Weak transcription	Fetal Stomach	stomach
41	chr10:98594600-98596200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr10:98594600-98596400	Enhancers	Primary B cells from cord blood	blood
43	chr10:98594600-98596800	Enhancers	Fetal Intestine Large	intestine
44	chr10:98594800-98596400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr10:98594800-98596400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:98594800-98596600	Enhancers	Fetal Intestine Small	intestine
47	chr10:98594800-98599400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr10:98594800-98600400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr10:98595000-98596600	Enhancers	Brain Anterior Caudate	brain
50	chr10:98595000-98597600	Enhancers	Fetal Heart	heart

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