Variant report

Variant	rs10197412
Chromosome Location	chr2:38981207-38981208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
2	chr2:38879772..38882593-chr2:38978947..38981476,2	K562	blood:
3	chr2:38980271..38983195-chr2:38988921..38991743,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000227238	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10173118	0.87[ASW][hapmap];0.89[CEU][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10173240	0.84[CEU][hapmap]
rs10865143	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1138975	0.82[ASN][1000 genomes]
rs11694383	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11898812	0.91[CHB][hapmap]
rs12469681	0.80[EUR][1000 genomes]
rs12472454	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12473036	0.80[EUR][1000 genomes]
rs12474770	0.93[ASN][1000 genomes]
rs12477252	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12618118	0.91[CHB][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621103	0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[ASN][1000 genomes]
rs12991609	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13014136	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13024811	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs13029406	0.86[ASW][hapmap];0.85[CEU][hapmap];0.81[TSI][hapmap]
rs13383541	0.84[CEU][hapmap]
rs13411868	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13417196	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1529625	0.85[CEU][hapmap];0.82[CHB][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs1530852	0.93[ASW][hapmap];0.92[CEU][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs1530853	0.93[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs1979142	0.85[CEU][hapmap]
rs1979143	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs1997377	0.87[MEX][hapmap]
rs2037875	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272445	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs3097713	1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap]
rs3097714	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs3099968	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap]
rs3099971	0.81[ASN][1000 genomes]
rs3112178	1.00[CHB][hapmap]
rs3112183	0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[ASN][1000 genomes]
rs3112184	0.91[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.81[ASN][1000 genomes]
rs3112186	0.81[ASN][1000 genomes]
rs3112188	0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.81[ASN][1000 genomes]
rs3112189	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs3112191	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs3112192	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs3112196	0.91[CHB][hapmap]
rs3112198	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3112200	0.89[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs3134628	1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[ASN][1000 genomes]
rs3134629	0.88[ASN][1000 genomes]
rs3134630	0.88[ASN][1000 genomes]
rs3134637	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs35387882	0.87[ASN][1000 genomes]
rs3731838	1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.82[ASN][1000 genomes]
rs4602206	0.96[CEU][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4630748	0.96[CEU][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4670891	0.86[AFR][1000 genomes]
rs4670892	0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs56393601	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62144837	0.83[AMR][1000 genomes]
rs6715866	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6717670	0.91[CHB][hapmap]
rs6728394	0.87[MEX][hapmap];0.83[TSI][hapmap]
rs6746818	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6753251	0.82[EUR][1000 genomes]
rs6756847	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs7419616	0.81[ASW][hapmap];0.96[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs7419838	0.89[CEU][hapmap]
rs7603676	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10197412	DHX57	cis	parietal	SCAN
rs10197412	DHX57	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979000-38981400	Weak transcription	Ovary	ovary
2	chr2:38979200-38981400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:38979200-38981400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:38979200-38981400	Weak transcription	Right Atrium	heart
5	chr2:38979200-38983800	Weak transcription	HSMM	muscle
6	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:38979400-38981400	Weak transcription	NHDF-Ad	bronchial
8	chr2:38979400-38981400	Weak transcription	Osteobl	bone
9	chr2:38979400-38981600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:38979800-38981400	Weak transcription	A549	lung
11	chr2:38980800-38981400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr2:38980800-38981600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:38980800-38982000	Enhancers	HepG2	liver
14	chr2:38980800-38982400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:38981000-38981400	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:38981000-38981400	Enhancers	Primary hematopoietic stem cells	blood
17	chr2:38981000-38981400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr2:38981000-38981400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:38981000-38981400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr2:38981000-38981400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:38981000-38981400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:38981000-38981400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:38981000-38981400	Enhancers	Fetal Intestine Small	intestine
24	chr2:38981000-38981400	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr2:38981000-38981600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr2:38981000-38981600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr2:38981000-38981600	Enhancers	Stomach Mucosa	stomach
28	chr2:38981000-38981800	Enhancers	Primary B cells from peripheral blood	blood
29	chr2:38981000-38982000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:38981000-38982000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:38981000-38982000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:38981200-38981400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:38981200-38981400	Active TSS	Primary T cells from cord blood	blood
34	chr2:38981200-38981400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr2:38981200-38981400	Enhancers	Duodenum Mucosa	Duodenum
36	chr2:38981200-38981600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:38981200-38981600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr2:38981200-38981600	Enhancers	Primary B cells from cord blood	blood
39	chr2:38981200-38981600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:38981200-38981600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr2:38981200-38981600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:38981200-38981600	Enhancers	Adipose Nuclei	Adipose
43	chr2:38981200-38981600	Flanking Active TSS	Liver	Liver
44	chr2:38981200-38981600	Enhancers	Dnd41	blood
45	chr2:38981200-38981600	Flanking Active TSS	GM12878-XiMat	blood
46	chr2:38981200-38982000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr2:38981200-38982000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:38981200-38982200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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