Variant report

Variant	rs7604835
Chromosome Location	chr2:152881908-152881909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152880919..152883751-chr2:153572245..153574813,2	MCF-7	breast:
2	chr2:152855344..152855911-chr2:152881823..152882603,2	MCF-7	breast:
3	chr2:152855213..152856214-chr2:152881741..152883020,10	K562	blood:

Variant related genes	Relation type
ENSG00000177917	Chromatin interaction
ENSG00000196504	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10930888	0.88[EUR][1000 genomes]
rs10930892	0.89[CEU][hapmap]
rs12471157	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12477734	0.83[AMR][1000 genomes]
rs12616521	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12619485	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16830598	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16830616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1949521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2139417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2345160	0.81[CHB][hapmap]
rs2881059	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35478891	0.87[EUR][1000 genomes]
rs3845845	0.90[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4146376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4362556	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4664075	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4664076	0.87[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.89[MEX][hapmap]
rs4664513	0.87[CHB][hapmap];0.84[MEX][hapmap]
rs4664519	0.82[TSI][hapmap]
rs58248711	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58402146	0.88[EUR][1000 genomes]
rs58761979	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61156093	0.88[EUR][1000 genomes]
rs6433726	0.87[CHB][hapmap]
rs6433777	0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs6721518	0.87[CHB][hapmap]
rs6728019	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6748530	0.81[CHB][hapmap]
rs6755776	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs72621651	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7607341	0.81[CHB][hapmap]
rs7607695	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs9917162	0.88[EUR][1000 genomes]
rs9917211	0.88[EUR][1000 genomes]
rs9917218	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv875290	chr2:152803129-152920126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7604835	TNFAIP6	cis	parietal	SCAN
rs7604835	C11orf17	trans	cerebellum	SCAN
rs7604835	STAM2	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152872400-152882200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:152877000-152882000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:152879000-152882000	Weak transcription	Brain Angular Gyrus	brain
4	chr2:152879000-152882200	Weak transcription	GM12878-XiMat	blood
5	chr2:152879000-152887600	Weak transcription	Fetal Brain Male	brain
6	chr2:152879400-152882200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:152881600-152882200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:152881800-152882000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:152881800-152882000	Flanking Active TSS	HUVEC	blood vessel
10	chr2:152881800-152882200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:152881800-152882200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:152881800-152882200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:152881800-152882200	Enhancers	Primary hematopoietic stem cells	blood
14	chr2:152881800-152882200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr2:152881800-152882200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:152881800-152882200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:152881800-152882200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr2:152881800-152882200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr2:152881800-152882200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:152881800-152882200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:152881800-152882200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:152881800-152882200	Enhancers	Brain Anterior Caudate	brain
23	chr2:152881800-152882200	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:152881800-152882200	Enhancers	Brain Hippocampus Middle	brain
25	chr2:152881800-152882200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:152881800-152882200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr2:152881800-152882200	Enhancers	Fetal Kidney	kidney
28	chr2:152881800-152882200	Enhancers	Dnd41	blood
29	chr2:152881800-152882200	Enhancers	HepG2	liver
30	chr2:152881800-152882600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:152881800-152882600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:152881800-152882600	Active TSS	Brain Substantia Nigra	brain
33	chr2:152881800-152882600	Enhancers	Placenta	Placenta
34	chr2:152881800-152883000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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