Variant report

Variant	rs4536500
Chromosome Location	chr16:75343197-75343198
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75343100-75343211	HepG2	liver:	n/a	n/a
2	CTCF	chr16:75343120-75343270	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75342449..75344190-chr16:75344958..75347399,2	K562	blood:
2	chr16:75339483..75341354-chr16:75341556..75343894,3	K562	blood:
3	chr16:75341957..75345575-chr16:75345642..75348406,3	MCF-7	breast:
4	chr16:75284253..75286453-chr16:75342020..75344397,2	MCF-7	breast:
5	chr16:75296329..75299018-chr16:75342294..75345279,2	MCF-7	breast:
6	chr16:75342673..75344343-chr16:75413150..75415792,2	MCF-7	breast:
7	chr16:75339157..75341354-chr16:75341501..75344826,6	K562	blood:
8	chr16:75338626..75341823-chr16:75342564..75345617,5	MCF-7	breast:
9	chr16:75272479..75274347-chr16:75342117..75343955,2	MCF-7	breast:

No data

Variant related genes	Relation type
CFDP1	TF binding region
ENSG00000050820	Chromatin interaction
ENSG00000261783	Chromatin interaction
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs1017239	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10514393	0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs10514396	0.83[JPT][hapmap]
rs1074961	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10781977	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10871307	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10871308	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1109342	0.83[JPT][hapmap]
rs11149812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11149813	0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11149814	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11149815	0.88[JPT][hapmap]
rs11149816	0.93[ASN][1000 genomes]
rs11149831	0.83[JPT][hapmap]
rs11641532	0.82[CHB][hapmap]
rs11645329	0.81[ASN][1000 genomes]
rs11645691	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11646418	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12149063	0.83[JPT][hapmap]
rs12445188	0.96[ASN][1000 genomes]
rs12445211	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12445813	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12446903	0.91[ASN][1000 genomes]
rs12449177	0.97[ASN][1000 genomes]
rs12922897	0.81[ASN][1000 genomes]
rs12932952	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12935329	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13337397	0.80[MEX][hapmap]
rs1364078	0.84[JPT][hapmap]
rs1549306	0.83[JPT][hapmap]
rs17696696	0.83[JPT][hapmap]
rs185052	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs1862705	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1862706	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1895489	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1895490	0.83[JPT][hapmap]
rs2032926	0.94[ASN][1000 genomes]
rs2059256	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2059257	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242405	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs247423	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs247424	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs247425	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs247427	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247431	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247434	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247436	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247437	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247438	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247447	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap]
rs2865527	0.87[ASN][1000 genomes]
rs2865530	0.83[JPT][hapmap]
rs2865531	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2865532	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2903033	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs35263058	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs3743606	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3743614	0.80[MEX][hapmap]
rs37602	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs3784936	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784937	1.00[ASN][1000 genomes]
rs3844219	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851733	0.83[JPT][hapmap]
rs3851735	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851736	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3851739	0.80[ASN][1000 genomes]
rs3863445	0.82[JPT][hapmap]
rs4146809	0.83[JPT][hapmap]
rs4146810	0.82[JPT][hapmap]
rs42472	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs455407	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4638613	0.83[JPT][hapmap]
rs467223	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs467780	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs468079	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4887812	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4887813	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4887814	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4887823	0.82[JPT][hapmap]
rs4887824	0.83[JPT][hapmap]
rs4887828	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs4888369	0.82[EUR][1000 genomes]
rs4888370	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888371	0.85[ASN][1000 genomes]
rs4888374	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4888375	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4888379	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4888380	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs4888381	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4888383	0.83[JPT][hapmap]
rs4888386	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4888387	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4888388	0.83[JPT][hapmap]
rs4888389	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4888393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4888394	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4888395	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4888396	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4888397	0.88[ASN][1000 genomes]
rs4888398	0.91[ASN][1000 genomes]
rs4888405	0.83[JPT][hapmap]
rs4888415	0.82[JPT][hapmap]
rs4888416	0.83[JPT][hapmap]
rs4888430	0.80[CHB][hapmap]
rs4993971	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6564245	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6564249	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6564256	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7187263	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7187690	0.93[CEU][hapmap]
rs7188604	0.83[JPT][hapmap]
rs7189407	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7192155	0.91[ASN][1000 genomes]
rs7199132	0.81[JPT][hapmap]
rs7199680	0.88[ASN][1000 genomes]
rs7202284	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7203157	0.83[JPT][hapmap]
rs766521	0.83[JPT][hapmap]
rs766522	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8046109	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs8046184	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8046416	0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs8046949	0.91[ASN][1000 genomes]
rs8047811	0.84[ASN][1000 genomes]
rs8048677	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8048816	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8049611	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8050059	0.83[JPT][hapmap]
rs8050662	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8051611	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8051785	0.92[ASN][1000 genomes]
rs8053632	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8054586	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8055609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs889446	0.91[JPT][hapmap];1.00[ASN][1000 genomes]
rs9922008	0.81[ASN][1000 genomes]
rs9933956	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9934007	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9989421	0.91[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	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	nsv833283	chr16:75302175-75392308	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4536500	TMEM170A	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75317400-75358000	Weak transcription	Fetal Brain Male	brain
2	chr16:75332600-75352000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:75335000-75346400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr16:75336000-75346600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:75336800-75346600	Weak transcription	Ovary	ovary
6	chr16:75338800-75346600	Weak transcription	Fetal Brain Female	brain
7	chr16:75338800-75349400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr16:75338800-75349800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr16:75338800-75351200	Weak transcription	Right Ventricle	heart
10	chr16:75338800-75426400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr16:75339000-75346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:75339000-75347000	Weak transcription	Lung	lung
13	chr16:75339200-75358000	Weak transcription	Brain Germinal Matrix	brain
14	chr16:75339400-75411800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr16:75339600-75343400	Weak transcription	Primary B cells from cord blood	blood
16	chr16:75339600-75343400	Enhancers	Fetal Muscle Leg	muscle
17	chr16:75339800-75346800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr16:75339800-75347000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr16:75339800-75347000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr16:75340000-75344200	Enhancers	Pancreas	Pancrea
21	chr16:75340000-75353200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr16:75340200-75343600	Enhancers	Fetal Intestine Large	intestine
23	chr16:75340200-75353000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr16:75340200-75353200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr16:75340400-75343400	Enhancers	Dnd41	blood
26	chr16:75340400-75344600	Enhancers	Stomach Mucosa	stomach
27	chr16:75340400-75345200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr16:75340400-75345200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr16:75340400-75345400	Weak transcription	Fetal Stomach	stomach
30	chr16:75340400-75346800	Weak transcription	Adipose Nuclei	Adipose
31	chr16:75340400-75347400	Weak transcription	Thymus	Thymus
32	chr16:75340400-75349600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr16:75340400-75351000	Weak transcription	GM12878-XiMat	blood
34	chr16:75340400-75353200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr16:75340400-75374800	Weak transcription	Aorta	Aorta
36	chr16:75340600-75343800	Weak transcription	HSMMtube	muscle
37	chr16:75340600-75345600	Weak transcription	Colon Smooth Muscle	Colon
38	chr16:75340600-75346400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr16:75340600-75347800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr16:75340600-75352600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr16:75340600-75352800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr16:75340600-75353000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr16:75340600-75354200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr16:75340800-75343800	Weak transcription	Fetal Kidney	kidney
45	chr16:75340800-75344600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr16:75340800-75345200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr16:75340800-75345200	Weak transcription	Osteobl	bone
48	chr16:75340800-75346800	Weak transcription	Primary T cells from cord blood	blood
49	chr16:75340800-75346800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr16:75340800-75347400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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