Variant report

Variant	rs7556029
Chromosome Location	chr1:171164111-171164112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171161907..171164775-chr1:171168366..171171218,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10912667	0.81[ASN][1000 genomes]
rs12121072	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12124505	0.92[ASN][1000 genomes]
rs12126946	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2020870	1.00[ASW][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2072756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28369802	0.88[ASN][1000 genomes]
rs28369803	0.88[ASN][1000 genomes]
rs28369818	0.92[ASN][1000 genomes]
rs28369863	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28369865	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28369918	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28384819	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6662994	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6662995	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6677549	0.80[ASN][1000 genomes]
rs7518693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519117	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7527067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7527478	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7539639	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7542361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7551282	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7556029	KIFAP3	cis	parietal	SCAN
rs7556029	FMO2	cis	parietal	SCAN
rs7556029	FMO3	cis	cerebellum	SCAN
rs7556029	RCSD1	cis	cerebellum	SCAN
rs7556029	GPR161	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171156400-171165800	Weak transcription	Gastric	stomach
2	chr1:171156600-171169800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:171156600-171177200	Weak transcription	Esophagus	oesophagus
4	chr1:171156600-171179600	Weak transcription	NHLF	lung
5	chr1:171156800-171179600	Weak transcription	Right Ventricle	heart
6	chr1:171157800-171165600	Weak transcription	Ovary	ovary
7	chr1:171158200-171167000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:171158400-171165600	Weak transcription	Fetal Lung	lung
9	chr1:171159000-171165800	Weak transcription	Lung	lung
10	chr1:171160000-171164800	Weak transcription	Fetal Intestine Small	intestine
11	chr1:171160000-171165000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:171160200-171166800	Weak transcription	Fetal Brain Male	brain
13	chr1:171161000-171165800	Weak transcription	Aorta	Aorta
14	chr1:171161000-171171800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:171161200-171165000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:171161800-171164200	Weak transcription	Liver	Liver
17	chr1:171161800-171165000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:171162600-171165800	Weak transcription	Right Atrium	heart
19	chr1:171163000-171167400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:171163400-171164200	Weak transcription	Stomach Mucosa	stomach
21	chr1:171163600-171166600	Genic enhancers	Adipose Nuclei	Adipose
22	chr1:171163600-171167200	Enhancers	Fetal Intestine Large	intestine
23	chr1:171163800-171165200	Enhancers	Small Intestine	intestine
24	chr1:171163800-171165600	Weak transcription	Psoas Muscle	Psoas
25	chr1:171164000-171165600	Weak transcription	Left Ventricle	heart

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